Brigadier General Feroz Khan’s presentation at the Naval Postgraduate School on Pakistan: Political Transitions and Nuclear Management
Feb 27, 2012
AUTHOR: Feroz Khan
Pakistan-Political Transitions and Nuclear Management (PDF) 106.11 KB
Pakistan: Political Transitions and Nuclear Management
By Feroz Hassan Khan
Throughout its history, Pakistan has experienced a number of dramatic political changes. Since the death of its founder Mohammad Ali Jinnah, who died 13 months after independence from British India, not one transfer of power has happened in an orderly manner. Jinnah’s death led to a succession of political leaders who have been assassinated, overthrown, or exiled. Pakistan’s political history is checkered with the dismissals of six Prime Ministers in the 1950s, four military coups, and four dissolutions of the parliamentary government using presidential constitutional powers.  In 1971, a major military defeat and the subsequent dismemberment of Pakistan forced President Yahya Khan to hand over power to Zulfiqar Ali Bhutto’s elected government. Another change occurred when President General Zia- ul- Haq’s plane crashed in August 1988.
Since its inception, Pakistan has had weak political and civilian structures, but a strong defense institution. With a prostrate economy, maintaining large defense forces and a nuclear program has proved challenging. These compulsions forced Pakistan to seek external alliances and military build up, but eventually these strategies could not prevent aggression or national dismemberment and Pakistan concluded that nuclear weapons were the only option for national survival.
Given Pakistan’s history of tumultuous political changes with simultaneous progress in the nuclear program for the past forty years, scholars and policy makers have often questioned the impact of leadership transitions on authority, decision- making, consistency of nuclear management, and ultimate control of nuclear arsenals in various periods of its nuclear history. For sixty years, Pakistan has vacillated between presidential and parliamentary forms of government. Generally, military rulers have preferred a presidential form of governance, believing in centralized control of the federal government and devolved power at the local (district) level while keeping provincial (state) government in check to prevent ethnic polarization and / or secessionism. Political leaders, on the contrary, traditionally support a parliamentary form of governance. Political parties prefer a federation with a central government whose powers pass to strong provincial governments with less power at the local level. The military fears such devolution builds corruption and results in provincialism, undercutting national unity, preventing progress at the grass roots level, and perpetuating feudalism. Meanwhile, the political leadership believes the presidential system could be manipulated at a local level to propagate authoritarianism and military rule.
Since Pakistan embarked upon its nuclear program, three key political transitions affected the nature of Pakistani nuclear management, which are analyzed in this paper. The military coup in July 1977 brought down the government of Prime Minister Zulfiqar Ali Bhutto. The next transition occurred eleven years later when President Zia- ul –Haq’s plane crashed along with the bulk of the ruling military leadership in August 1988. At the time, Pakistan had developed nascent nuclear capability. This was followed by a decade of democracy where political power was diffused between President, Prime Minister and the Chief of Army Staff (COAS), commonly referred as the “troika of power.” During this period, nuclear control shifted from the President to the COAS in 1993, when both the President and Prime Minister were forced to resign. Finally, General Musharraf‘s military takeover in October 1999 was the most dramatic of all other military coups. This event happened barely a year and half after Pakistan had demonstrated its nuclear weapons capability.
Apart from a minority liberal elites, often considered nuclear pessimists, within the broad spectrum of Pakistani politics and strategic community there is a strong consensus on the rationale for the role of nuclear weapons in national security and on the current structure of nuclear management. Each successive ruler since Zulfiqar Ali Bhutto initiated the program has advanced the nuclear program from where his / her predecessor left it. This pattern has continued regardless of any bitterness between successors and predecessors.
The vacillation of political authority between the President and the Prime Minister has allowed the COAS to become the arbitrator of national security policy. On nuclear matters specifically, the COAS became the most powerful sponsor on behalf of the military-scientific community until the national command authority was formally announced in February 2000. It is for this reason nuclear management remains unaffected by the turbulence of national political change, as this paper will show.
This chapter analyzes Pakistan’s political transitions in relation to their impact on the national nuclear program, the security of nuclear arsenals, and the evolution of a nuclear command –and- control system. The first section in this chapter analyzes Pakistani political transitions and nuclear management from the nation’s birth through its dismemberment as a unified country in 1971. Pakistan’s civilian program was established under unsettled political circumstances during which East Pakistan and West Pakistan were geographically separated by a hostile India. During this period, the military regimes of Ayub Khan and Yahya Khan resisted shifting the civilian nature of the nuclear program towards a military one.
The second section examines the period under the leadership of Zulfiqar Ali Bhutto, when the nuclear weapons program commenced. His ouster from power after a military coup marked the end of the civilian-controlled nuclear weapons program and brought a military-dominated command system during which Pakistan attained nascent nuclear weapon capability.
The third section studies the sudden transformation from a military system to a cycle of democratic regimes as a result of plane crash in which the entire leadership perished. For over a decade, the President, Prime Minister and COAS (the troika) shared political power while the nuclear program advanced covertly, under the guidance and support of the military.
The fourth section explains how perpetual political instability forced a two-phased transition back to military control. For a period of about six years (1993- 1999) the nuclear program remained under quasi-military control while President and Prime Minister jockeyed for political power. This quasi-control finally transited into a fully military-dominated system after the coup of 1999.
In the following decade after the 1998 nuclear tests, Pakistan force posture transformed from a demonstrated nuclear capability into an operational deterrent as a robust command and control system evolved during Musharraf’s era. The last political transition occurred with the return to civilian democratic rule in 2008. However, this period coincided with an extraordinarily violent phase in the country’s history that lasted from March 2007 till August 2008. Nevertheless, even as Pervez Musharraf departed the scene into exile, the nuclear command authority remained unscathed and the new government adopted the system, ensuring a smooth transition. The paper concludes that despite domestic instabilities and rough political transitions, by and large the control of the nuclear program has remained unaffected. The main reason for this is the general national consensus over the nuclear program and status.
1.00 POLITICAL TRANSITIONS AND NUCLEAR MANAGEMENT 1947- 1971
When the British left Pakistan in 1947, the birth of a new nation took place in a massive vacuum, caused by factors such as a leadership crisis, weak political institutions, a non-existent constitutional direction, and economic challenges. At partition in 1947, Pakistan was distressed when an unfair distribution of assets was compounded by India’s refusal to deliver Pakistan’s due share. As one author described, “Pakistan inherited a paper army and skeleton navy and air force.” Despite that, the professional military structure, which became Pakistan’s armed forces, comprised well-trained officers and educated junior commissioned officers. In contrast, social institutions were weak or non-existent; feudal lords and tribal leaders wielded power, much of the population was uneducated, and ethnic groups were polarized. This structural imbalance has plagued Pakistan throughout its history.
Failure to establish a viable political system in the first decade of its existence led to the military coup in 1958, which set the pattern for all future military take-overs. The military institution quickly became a vital stakeholder in Pakistan’s governance system and security policy. Referred to as the “establishment,” the Pakistani military is believed to have a nationalist vision of security and its nuclear program, which by and large has remained constant despite the uncertain political progress in Pakistan. 
Atomic science in 1950s was a low priority for the policy-makers in Pakistan. Consolidating the nation-state was monumental task as the country recovered from traumatic partition. Pakistan was veritably beginning nation- building from the scratch in the absence of strong leadership, due to the death of the nation’s founder. Facing multitudinous domestic political instabilities, regional crises with neighbors, and lacking adequate infrastructure, Pakistan was barely surviving as a nation-state. The U.S. military alliance (SEATO and CENTO) and the military take-over of the national leadership in 1958 gave the nation a semblance of stability and new direction towards national development. Though by the mid- 1960s the nation was stable and prospering economically, its political structures remained weak, and resentment and polarization was growing between West Pakistan and East Pakistan.
Under these disturbing political conditions, Pakistan’s nuclear program was founded in the mid-1950s. President Eisenhower’s Atoms for Peace initiative induced interest in nuclear energy. The Pakistani government established a 12 member Atomic Energy Committee, comprised of scientists and technical specialists to study the feasibility of and prepare blueprints for peaceful uses of atomic energy. When the Pakistan Atomic Energy Commission (PAEC) was formed in 1956, the chairman reported to a relatively junior officer in the Ministry of Industries and had no direct access to the chief executive. The civil bureaucracy (planning division and ministry of finance) had an apathetic attitude towards the scientific bureaucracy from the very beginning. Despite its lesser importance the scientific bureaucracy was somewhat autonomous in nuclear decision-making. 
It was not until a young Zulfiqar Ali Bhutto became minister of Fuel, Power and Natural Resources, that political interest and insight in the Pakistani atomic energy program emerged. Bhutto later wrote: ”When I took charge of Pakistan’s Atomic Energy Commission, it was no more than a signboard of office.” He explained how under his stewardship he “put his entire vitality behind the task of acquiring nuclear capability for my country.” 16] The combined efforts of Bhutto, Dr. Abdus Salam, an eminent physicist and advisor to the President on Science and Technology, and Dr. Ishrat Hussain Usmani, the Chairman of the PAEC enabled Pakistan to send hundreds of young men to top Western universities to train in the new atomic sciences.
Around the mid-1960s, most Western-qualified scientists in Pakistan believed that genuine interest in nuclear energy would only come about if the top leadership was convinced to develop nuclear weapons. They surmised that atomic science found national priority only in countries where a strong lobby and rationale for national defense existed. Additionally, the military would be easily convinced if the argument emphasized an impending nuclear threat from India, which had embarked on its own nuclear program at the time. Some bureaucrats in the Pakistani foreign ministry and a few scientists approached General Ayub Khan about broadening the horizon of the nuclear program and acquiring technologies that would meet not just the energy needs but potential national security and defense needs as well. These proposals were met with resistance.
As Foreign Minister (1963-1966), Bhutto urged President Ayub Khan to purchase nuclear power reactors and a reprocessing plant from France. Bhutto argued that India was proceeding ahead with nuclear weapons development after China’s test in 1964 and the window of technological availability was short as deliberations on the non-proliferation treaty drew to a close.
General Ayub Khan disappointed the bomb enthusiasts, however. His concern was that any move towards obtaining such technologies would jeopardize the country’s Western alliance. Pakistan boasted an impressive economic growth (averaging over 6 percent GDP). Meanwhile, conventional military modernization was continuing apace and was thought to be best deterrent for national defense. Lastly, access to peaceful uses of nuclear energy under the Atoms for Peace was forthcoming, both in the realm of the soft technologies (scientists, developing a cadre of trained manpower and technical know-how) as well as hard technologies (power reactors and a technological base for nuclear science).
President Ayub’s focus on national development was disastrously affected by his decision to approve the covert guerrilla operations in Kashmir (Operational Gibraltar) in the hope of igniting an uprising with a follow-up military operation (Operation Grand Slam). India subsequently attacked Pakistan and war broke out in September 1965. Ayub would take no further risks. Bhutto, in close concert with senior army generals, had designed the aggressive Kashmir policy. Ayub‘s lack of judgment in 1965 derailed Bhutto’s nuclear ambition.
Ayub feared the alliance with the United States was in jeopardy, especially after his meeting with President Johnson in December 1965 when he learned of diminishing U.S. interest in South Asia. Indeed the United States had willingly abdicated the responsibility of bringing peace to the region to the Soviet Union. In January 1966, the Soviet Union mediated a peace agreement between India and Pakistan at Tashkent. 
Subsequent attempts to persuade Ayub’s successor, General Yahya Khan to further nuclear capability also failed. Yahya Khan was too consumed with domestic crises to focus on any other aspect at the time. The so-called “bomb lobby” blamed the military leadership for failure to grasp the changing regional strategic environment. They remained critical of the faith in American led security alliances (SEATO and CENTO), which had given a false sense of confidence for national defense against India’s intentions and conventional force capability.
BHUTTO”S NUCLEAR PROGRAM AND ZIA COUP 1971- 1977
Zulfiqar Ali Bhutto was undoubtedly the political father of the Pakistani bomb. Within a month of assuming power following the catastrophic military surrender in Dhaka in December 1971, President Bhutto summoned a meeting of all scientists in Multan on January 20,1972. The main purpose of the meeting was to remove the incumbent Chairman PAEC, I.H.Usmani, who Bhutto believed had little interest in pursuing the nuclear weapons program. Bhutto replaced him with his friend and confidante, Munir Ahmad Khan, formerly Director of the International Atomic Energy Commission (IAEA), who had worked on plutonium reactors. Bhutto’s objective was to indicate the shift in the nature of the nuclear program. Bhutto was aware that the wherewithal needed for nuclear capability would take time. He simply wanted to boost the morale of the scientists and let it be known that the new government meant business.
It was in 1974, however, after India’s nuclear test, when Bhutto’s strategy of a slow-and-subtle acquisition of nuclear capability transformed into a crash nuclear weapons program. Bhutto was angry at the program’s slow progress, and so brought the entire civil and military leadership into confidence, galvanizing the nuclear program to the highest national priority. After India’s test on May 19, 1974, Bhutto held a press conference in Lahore and stated:
“There is no need to be alarmed over India’s nuclear demonstration… Let me make it clear that we are determined not to be intimidated by this threat. I give a solemn pledge to all our countrymen that we will never let Pakistan be a victim of nuclear blackmail.”
Bhutto had always tightly controlled the nuclear program for secrecy. He had become the Prime Minister after the new parliamentary system was put into effect under the 1973 Constitution of Pakistan. Once Prime Minister, he had little time to devote to the program since he was focused on many national issues. Bhutto constituted an inter-ministerial committee of senior ministers, bureaucrats, and scientists. The committee had no formal title or name so as to maintain its secrecy, but the main purpose was to ensure continued progress of the nuclear program and remove any bureaucratic obstacles or snags, particularly in finances and procurement of technologies. The pivotal person who tightly coordinated this inter-ministerial group was Major General Imtiaz Ali, Military Secretary to Prime Minister Bhutto.
Throughout the Bhutto era, decision-making on the nuclear program did not involve the military leadership. Bhutto kept the military away as a means to maintain civilian control of national security, particularly in regards to the nuclear program, and domestic politics. The military as an institution, however, provided all the resources and assistance that the PAEC needed. Later, when the construction of Engineering Research Laboratories commenced, the military provided manpower and equipment from its technical branches such as Corps of Engineers, Electrical and Mechanical Engineers (EME), and Signals and Aviation. The Military Operational Directorate and logistical branches of General Headquarters played supporting roles in helping select sites for future tests. Military ordnance factories provided space for housing centrifuge facilities and supplied knowledge for explosives trainings. The Army’s logistical branches provided barracks and ammunition depots to start the centrifuge program. The military was well aware of the nature of the classified project even though it was not privy to the technical details, blueprints, or objectives of the program. 
Prime Minister Bhutto later convinced Dr. Abdul Qadeer Khan, a Pakistani scientist, to return from Holland to run the centrifuge program. In the summer of 1976, Bhutto directed the separation of the centrifuge project from PAEC and gave AQ Khan independent responsibility, free from any pressures. Bhutto promised open-ended funding to AQ Khan to complete the task as well as direct access to the Prime Minister, a privilege until then only enjoyed by the Chairman of the PAEC. Every embassy and national institution was involved in procuring resources from abroad and substituting resources from inside the country to get the weapon to completion. In 1981, one of the primary nuclear facilities was named after AQ Khan, the Khan Research Laboratory (KRL).
By the spring of 1977, Prime Minister Bhutto was consumed with his reelection campaign and, though he won the elections, he had rigged them unnecessarily. This triggered massive protests from the opposition, a coalition of nine right-wing political parties, which mounted a massive campaign to oust Bhutto from power in the summer of 1977. Bhutto summoned the military to control the protest, resulting in a temporary martial law in Lahore, foreshadowing the military-take over in July 1977.
After the bloodless military take-over, General Zia-ul- Haq became the Chief Martial Law Administrator (CMLA). Prime Minister Bhutto and his family were taken into “protective custody” at the nearby hill station in Murree. A few days later, the new military leader visited his former Prime Minister and discussed the future course of action, which included holding elections within 90 days, as stipulated in the constitution. But Zia reneged on the promise to hold elections in three months time. Instead, he decided to become President and formed an interim government, bringing in several ministers who were members from Jamaat-i-Islami, a religious political party that was in forefront in opposition against Bhutto throughout the summer of 1977. Meanwhile, Bhutto faced trial for abetting the murder of a political opponent.
Z. A. Bhutto was concerned that the nuclear weapons program was adversely affected by Zia-ul- Haq’s coup. He doubted Zia had the ability, much less the vision, to see it through. It was possible Bhutto did not trust that the military even had interest in it, given his experience with Ayub and Yahya Khan. He may have concluded that Zia might barter away the nuclear weapons with conventional weapons to expand the army or simply get some financial aid to support the ailing economy, essentially the same rationale as was given in the 1960s.
Bhutto had negotiated the reprocessing plant deal with France, which he believed was due to his personal rapport with President Giscard d’Estaing and that he had satisfied the international community with the safeguard agreement. Bhutto was convinced that had he remained Prime Minister, France would not have backed out of the reprocessing plant agreement. On August 23, 1978, when President Zia-ul- Haq admitted that France had politely defaulted on the reprocessing plant, Bhutto responded that, ”The French had concluded the agreement with a civilian and constitutional government, not with a military and dictatorial regime… what does the [Zia-ul- haq] regime propose to meet the threat of this qualitative change? More Foreign Aid? Now that it is officially admitted that nuclear reprocessing plant is lost, with or without foreign aid, Pakistan would have to unquestionably move towards steeper dependence and alien-reliance… it will be more at the mercy of those who are professionals in the art of nuclear blackmail… what a fall, my countrymen! What a shattering blow to the dream of a lifetime.” 
When General Zia-ul-Haq overthrew the government of Zulfiqar Ali Bhutto in 1977, the nuclear weapons program (highly enriched uranium) was in its nascent stages. PAEC, however, continued building the infrastructure for completion of the nuclear fuel cycle. Military take-over in 1977 marked the first transition from civilian-dominated control of the nuclear program to a military-dominated one, which lasted over a decade. Under General Zia-ul-Haq, a unified command system evolved because he held both the office of the President and COAS.
Like Bhutto, Zia-ul–Haq took personal charge of the nuclear program. Zia, however, retained the same core senior civil servants in the coordination committee and also brought the military and scientific communities together, further shrouding the program. He removed Major General Imtiaz Ali, Bhutto’s Military Secretary, from all nuclear and sensitive dealings. Zia-ul-Haq received all briefings from two scientists, Munir Ahmad Khan and AQ Khan. He also retained the two most important persons, Defense Secretary Ghulam Ishaq Khan and Foreign Secretary Agha Shahi, in the inter-ministerial committee.
Zia appointed Lt. General Khalid Mahmood Arif as his Chief of Staff, an office that became the focal point of all coordinating activities, and all nuclear matters were transferred to his office from the Prime Minister’s office, which was closely connected with his Military Secretary. General Arif who explained the existence of a nuclear supervisory board under the chairman Mr. Ghulam Ishaq Khan and members Mr. Munir Ahmad Khan (Chairman PAEC), Dr. Ishfaq Ahmad (later chairman PAEC 1991- 2001), Dr. AQ Khan (Director KRL), Mr.H.u.Beg (Finance Secretary), and Mr. Bhutti(Finance Advisor).
General Zia-ul-Haq made all decisions and issued personal directives in close consultation with his team of Ghulam Ishaq Khan, Agha Shahi and General Arif, who ensured the continuity of the nuclear program. Initially, Zia had some doubts about the loyalty of PAEC Chairman Munir Khan, who was a protégé of Bhutto.  Zia also feared infiltration of Western spies into the nuclear program. He directed scientific organizations and intelligence agencies to keep a close eye on an “insider threat,” which could have been a mole in the program that would sabotage the program from within or facilitate an attack from the outside. Zia directed the army to undertake the defense of Kahuta centrifuge plant and the Karachi Nuclear Power Plant (KANUPP) installations. Such fears began after reports that the U.S. was contemplating a preventive strike surfaced in late 1979. These fears gained more credence after Israeli planes attacked and destroyed an Iraqi power plant at Osiraq in 1981.
Throughout the 1980s, the Pakistani nuclear program steadily progressed, though Zia-ul–Haq downplayed the nuclear card by insisting on its peaceful nature. Zia had made a secret agreement with President Reagan that he would not embarrass Reagan by pursuing any nuclear activity. The U.S. had given four nuclear restraint requirements to Pakistan: not to conduct hot tests; not to enrich low enriched to high enriched uranium; not to machine existing stocks into core; and not to transfer any know-how or material to any entity or state.
President Zia’s plane crashed on August 17, 1988. Along with him was the U.S. ambassador to Pakistan, Arnold Raphael, and Defense Attaché as well as several other Pakistani military leaders. Zia-ul-Haq had been both President and Chief of Army Staff. Under the country’s constitution, the Chairman of the Senate becomes the acting president, which in this case was Ghulam Ishaq Khan.
Under military rules of succession, General Mirza Aslam Beg, who had been Vice Chief of the Army Staff, automatically assumed the responsibility as acting Chief of Army Staff. General Beg had the option of declaring martial law and overruling the constitutional succession of the President. To his credit, however, Beg allowed the constitutional process to proceed. Thus, Senate Chairman Ghulam Ishaq Khan became the acting President of Pakistan. President Khan then formally named General Mirza Aslam Beg to become the Chief of the Army Staff. He also appointed the Chief of Naval Staff Admiral Iftikhar Sirohi as the Chairman of the Joint Chiefs of Staff in place of General Akhtar Abdul Rehman, who had also died in Zia’s plane crash.
This was the second major change in the system after the nuclear weapons program had commenced. Pakistan had developed enough fissile material to put together a few devices at short notice. Though Zia had agreed on nuclear restraint with President Reagan, there was no mechanism to assess its implementation. Zia prohibited nuclear explosion tests (hot tests), however, he allowed scientists to carry out cold tests and research and development on bomb designs and delivery means. Like his predecessor Bhutto, Zia had tightly controlled the nuclear program, making all related decisions personally. General K.M. Arif as Vice Chief of Army Staff was in the loop of nuclear knowledge and responsibility, but that was not an institutional arrangement. It was so because General Arif was President Zia’s Chief of Staff. Arif’s successor General Mirza Aslam Beg who was Vice Chief of the Army Staff from March 1987 till August was not privy to the details of the nuclear program. It was only after his appointment as the COAS in 1988, he became a central player in nuclear development and related decisions.
After Zia’s death the nuclear responsibility naturally acceded to the most knowledgeable and experienced man in the country. President Ghulam Ishaq Khan had institutional memory and a role in the nuclear program since the beginning of the military takeover.
Together, President Ishaq Khan and COAS Beg guided the nuclear program, with Army Chief Beg coordinating on behalf of the President and providing defense of key atomic institutions as well as support from the army to facilitate the goals of the strategic organizations. The inter-ministerial committee disappeared, as offices of the President and the COAS managed decisions until the Prime Minister was elected, who then became the third pillar of decision-making. In his memoir, Musharraf wrote, “After Zia’s death in 1988, Ghulam Ishaq Khan took over as president. Since he was a civilian, he brought the army chief into the loop. From then on the chief of the army staff started managing our nuclear development on behalf of the president.”
Elections were held in November 1988 and, as expected, Benazir Bhutto won a plurality to form a government. In the aftermath of 1988 election, President Ghulam Ishaq Khan, and Army Chief General Mirza Aslam Beg emerged as the guarantors of the policies of the Zia era.
THE DECADE OF DEMOCRACY AND POWER TROIKA
The Pakistan People’s Party had barely ended the electoral victory celebration when the Army Chief Mirza Aslam Beg invited the leader Ms. Benazir Bhutto to discuss the modalities of power transitions. General Beg explained his role in ensuring fair and free elections and the return of democracy after years of rule. Beg assured Ms. Bhutto of full cooperation from the Army and in a detailed expose, explained the precarious regional and internal security situation. The Soviet withdrawal from Afghanistan was proceeding apace to meet the February 1989 deadline; tension between United States and Ayatulaah Khomeni and America were continuing despite the end of Iran – Iraq War; most importantly for the nuclear program, an unprecedented India-backed uprising in Kashmir had begun, which had severe implications for Pakistan. With end of Cold War in sight, the alliance with the United States was unclear.
Pakistan’s overall domestic situation was tense and fragile. In order to prevent further domestic turbulence, General Beg suggested continuity of policy and retention of key personalities in the government once power was handed over. The Army would fully back the Prime Minister if she agreed to: 1) Continue to support and elect President Ghulam Ishaq Khan; 2) Pledge not to seek revenge for her father’s death from General Zia-ul-Haq’s family; 3) Continue the services of Foreign Minister Sahibada Yaqub-Khan; 4) Not to meddle in the internal matters of the armed forces.
Beg emphasized that Bhutto was extremely intelligent and bright but still inexperienced and therefore needed the wisdom and guidance of President Ghulam Ishaq Khan who had a long distinguished career and, more importantly, had been a constant since the evolution of the nuclear program in her father’s time. The vast experience of Foreign Minister Sahibzada Yaqub-Khan would allow continuity of the country’s foreign policy, especially given the regional uncertainty. Finally, she needed to consolidate her position and would need constant help from the Army. Bhutto agreed to these conditions and was sworn in as Prime Minister.
Benazir Bhutto was young, charismatic and an international icon for her struggle against a conservative military dictator who hanged her father. Being the first female Prime Minister in a Muslim country with a nuclear program, she had extraordinary celebrity appeal. She had emerged as leader from the shadows of war and instability. Little had she understood that the office she assumed was not as powerful as her father’s had been in the 1970s. Indeed, despite being elected, Ms. Bhutto was in essence sharing power with the President and Army Chief. The terms she had agreed to in exchange for a smooth power transfer meant she could operate within the agreed framework with the President and the Army.
Benazir was new to the vicissitudes of statecraft and the role of state bureaucracy and a powerful military in national policy. The President represented the bureaucracy who had the ultimate power under the constitution to dismiss the prime minister as well as the parliament. Additionally, the Army held the key to national security policy and was the backbone of Presidential power.
The diffusion of power at the apex of national governance resulted in a troika of leaders: President, Prime Minister, and the COAS. This governance structure in the political system of Pakistan was not formal, but the execution of policy was based on the consensus of the three in principle. In reality, it was the President and Army Chief who wielded decisive power over the most critical security policy of the state, which included the nuclear policy. For the next decade, the Pakistani governance system functioned under this diffused structure, which saw three dismissals of governments (1990, 1993 and 1997), successively recycling the governments of Benazir Bhutto and Nawaz Sharif before the military coup in 1999.
In the context of nuclear management, the decade of democracy (1988 – 1999) was divided into two periods. The first half was during the tenure of President Ghulam Ishaq Khan (August 1988 – July 1993) when he was the ultimate authority on all decisions and financial approvals on all civil and classified projects. The President had the final say on all nuclear matters and the Army Chief supported and coordinated the nuclear program on his behalf.
Benazir Bhutto maintained that she was never kept fully in the loop on nuclear matters and claimed the President and Army did not trust her. In her state visit to Washington in June 1989, Prime Minister Bhutto agreed to receive a detailed briefing from CIA Director William H. Webster on the progress of Pakistan’s nuclear program. The President and the Chief of Army Staff were concerned about Prime Minister Bhutto’s distrust of her own country’s system, symbolized by her bid to seek an outside briefing from United States, a country that was opposed to the Pakistani nuclear program from the outset. From then on the President and Army Chief never trusted the Prime Minister. Thus, a cloud of suspicion loomed over the office of the Prime Minister. Subsequently, the President and COAS hid classified details of the program from Bhutto.
COAS, General Aslam Beg, denies Benazir Bhutto’s assertion that she was not informed and intentionally kept out of the loop regarding the nuclear program. In an interview with the author, General Beg said that both Chairman of the PAEC, Munir Ahmad Khan, as well as A. Q. Khan, Director Khan Research Laboratory (KRL) gave Bhutto a detailed briefing on the status of nuclear weapons program soon after she took office. He also maintained that the ruling troika (which Beg dubbed as the national command authority of the time) collectively agreed to a nuclear restraint policy in 1989, in which Benazir Bhutto’s consent was primary. This policy involved capping the production of weapons grade uranium and only permitting KRL to enrich up to low enriched uranium (LEU); prohibiting turning the existing stock of highly enriched uranium (HEU) into bomb cores; not conducting hot tests; not transferring any technical know how or technology to a third party or country. Benazir Bhutto made a public commitment to the U.S Congress on her state visit to Washington D.C in 1989. In substance, this restraint policy was no different than the pledge General Zia-ul-Haq had secretly made to the Reagan administration in 1981.
Scientific experiments for delivery as well as cold tests of nuclear weapons designs continued well into the 1990s. Far from exercising restraint, the two scientific organizations involved in the nuclear program, PAEC and KRL, accelerated their competition to out-do the other. The triangular diffusion of authority allowed the scientific bureaucracy to exploit it. Most importantly, the absence of one authority created the conditions where AQ Khan was able to bypass all three powers by playing one against the other. Khan conducted his illicit activities independently. 
Benazir Bhutto’s government was dissolved in August 1990 after months of tensions between the President and Prime Minister. After a brief interim government, Nawaz Sharif was elected Prime Minister. Sharif was a prodigy of President Zia-ul- Haq and was expected to have a harmonious relationship with the military. He, however, was soon involved in tension with both the President as well as successive army chiefs until he was removed in 1993. After a brief interim government, Benazir Bhutto returned to power by the end of the year. She ruled for about three years when President Farooq Leghari dismissed her government in 1996, only for her rival Sharif to return in 1997. Sharif made constitutional amendments to make it impossible for the president to dismiss the parliament. After three years, the military removed Sharif from power, completing a full circle.
Despite political instability and jockeying for political power amongst the leadership, the nuclear program continued. This strengthened the nexus between the military, scientific and civil bureaucratic communities in Pakistan. The three communities developed a synergy of thoughts and action over nuclear policy and provided considerable autonomy to the scientific organizations to achieve national goals.
FROM PRESIDENCY TO MILIUTARY CONTROL
The political transition in July 1993 is significant from the nuclear management standpoint. In early 1993, after several months of a bitter power struggle between President Ghulam Ishaq Khan and Prime Minister Nawaz Sharif, the Chief of Army Staff General Abdul Waheed intervened and pressured both to resign from the office.
The crises between President and the Prime Minister had been brewing over several months, especially after the sudden death Chief of the Army Staff General Asif Nawaz in January 1993, who had succeeded General Aslam Beg in August 1991. General Asif Nawaz strictly kept his profile as professional army chief and never made any public comments on nuclear issues, which was always deferred to President Ghulam Ishaq Khan.
President Ishaq Khan appointed General Abdul Waheed as the new Army Chief. Apparently this choice was against the preference of Prime Minister Sharif, who considered his recommendation was binding on the President. This, amongst other issues, eventually led to a political crisis in April 1993, when Prime Minister Sharif publicly accused President Ghulam Ishaq Khan of undermining his executive authority. After series of accusations between the two, President Ishaq Khan dismissed Prime Minister Sharif’s government and parliament. This was the second time President Ishaq Khan exercised his power and the third in a row since late President Zia-ul- Haq had dismissed Prime Minister Mohammad Khan Junejo in May 1988. In all cases, the power exercised to dismiss the government and parliament was authorized under the 8th amendment of the constitution.
As always, the dismissal was challenged in the Supreme Court, but unlike in the past, the Supreme Court ruled in favor of the ousted Prime Minister and ordered restoration of the government in May. Sharif returned to office. For three months the tug of war continued between the two highest office of the country, each exercising its powers to demonstrate the locus of real political power, which almost brought the functioning of the state and government almost to a halt. As in the past, public figures looked to the Army, the most powerful institution in the country. Finally, in July 1993, Army Chief General Abdul Waheed stepped in to tell both the Prime Minister and President that enough was enough and it was time for both to leave.
With the resignation of both President and Prime Minister, a power vacuum both at the state level (the President) as well as the government level (the Prime Minister) was created. Under the constitution, the Chairman of the Senate Mr. Waseem Sajjad became the acting President and Mr. Moeen Qureshi, a former vice president of the World Bank, who was living in Washington D.C. at the time was made the interim prime minister for three months. The task of the interim government was to hold free and fair parliamentary elections in October 1993 and hand over power to the new elected government.
President Ghulam Ishaq Khan who was custodian of the nuclear program until then could not trust the interim arrangement and the political future was uncertain at the time. He handed over the responsibility of the classified nuclear weapons program including all documents to the Army Chief General Abdul Waheed. For the first time the nuclear responsibility and records were transferred from the office of the President to Pakistan’s Army General Headquarters (GHQ). General Abdul Waheed asked Major General Ziauddin in GHQ to take charge of the documents and coordinate with the nuclear program on his behalf. From July 1993 till December 1998 all nuclear issues were coordinated at the Combat Development Directorate (CD Directorate) in GHQ after which a new set up the strategic plans division (SPD) was established, which would later became the secretariat of the national command authority and functions as such to date.
From 1993 through 1999 until the military formally took political power, GHQ was the custodian of sensitive documents and coordinator of the nuclear program, even though political power continued to vacillate between the President and Prime Minister. Benazir Bhutto returned to power after the October 1993 elections after her party, Pakistan’s People’s Party (PPP) won plurality in the parliament. Ms. Bhutto nominated a PPP stalwart, Farooq Ahmad Leghari, to become the new elected president. Ms. Bhutto would have preferred the powers of the President under the 8th amendment to be clipped so as to make the Prime Minister strong, but she did not have enough support in the parliament to bring about the constitutional change.
For the next three years, political harmony existed amongst the power troika. The nuclear program coordination remained de facto with the Army, though the de jure authority rested with the Prime minister (being the chief executive under parliamentary system). Yet still the constitutional powers conferred to the president made him the supreme commander of the armed forces. Under the parliamentary norms, the president must act under advice of the prime minister, but in reality it was the power to dismiss the government made him anything but a ceremonial head. Yet this power could only be executed when in President’s judgment both the army as well as the supreme court of Pakistan was amenable for the dismissal of the prime minister.
Under such circumstances and given her previous experience as Prime minister, Benazir Bhutto preferred not to ruffle feathers with the military-civil bureaucratic- scientific nexus that were managing the nuclear program, an arrangement which by and large was politically acceptable to all. Thus, it suited both the President and Prime Minister to let GHQ be the locus of coordination and resources. But despite this tacit understanding, the military did not have the legal authority to intervene in the autonomy of the scientists, who had direct access to any of the troika of power. This diffusion is what caused not one single authority to have final oversight, until after General Musharraf’s coup, when institutional control of scientific organizations were made effective through both de jure and de facto measures.
By late 1996, President Farooq Leghari had reached a saturation point with the corruption, nepotism, and law and order inefficiency. He finally exercised his powers to dismiss the government of Benazir Bhutto, from his own erstwhile political party. This was the fourth dismissal in a row since the 8th amendment was exercised in 1988.
Once again the elections were held in 1997 which brought Nawaz Sharif back to power with an overwhelming majority in the parliament. Sharif promptly moved in the parliament to amend the constitution with the 13th amendment that took away the president powerless to dismiss the government under the previous 8th amendment.
In 1997, Prime Minister Nawaz Sharif emerged as the most powerful political prime minister since Zulfiqar Ali Bhutto in the 1970s. By the end of the year Sharif ousted incumbent President Farooq Leghari and also replaced the Chief Justice Sajjad Ali Shah of Supreme Court after power struggle renewed between President and prime minister. This time the struggle involved the Supreme Court in a bid to dismiss a powerful prime minister whose arbitrary and personalized style of governance and rampant corruption had seemingly no check.
Under the leadership of General Jehangir Karamat, Chief of the Army Staff since 1996, the army steered away from the political feud in Islamabad in 1997. With maximal political power with the Prime Minister in 1998, nuclear decision-making rested with the Prime Minister, but the nuclear coordination continued to be with GHQ (CD Directorate). During this period, Pakistan’s nuclear program made significant progress. It enhanced the fissile stocks, acquired bomb delivery capability through fighter aircraft, acquired and tested both solid and liquid ballistic missiles, and conducted nuclear tests in May 1998.
By October 1998, after a tense summer which involved nuclear tests and resultant nuclear sanctions, Prime Minister Sharif attempted absolute control when asked the Army Chief to resign from office. Sharif’s personalized style of governance was under criticism from all quarters in the country, which required a shift because Pakistan was now a declared nuclear power and informed decision-making was the need of the hour.
Sharif replaced Karamat with General Musharraf in October 1998. Within few months civil-military relations went sour, especially after the Kargil crisis with India that resulted in much bloodshed and regional tension within a year of the nuclear test, but the civil-military relations broke down, eventually leading to a military coup. This brought an end to the era of democracy and domestic instability.
General Pervez Musharraf led the last military coup in October 1999; the first power transition after Pakistan had declared itself an overt nuclear power. This transition returned the unity of command that had existed in the Zia era when the President wore both hats, that of the President as well as Army Chief.
In terms of nuclear control and coordination, the military coup did not affect the functioning, but strengthened the Strategic Plans Division (SPD), which had succeeded the role of Combat Development (CD) Directorate in GHQ. After taking over as Army Chief, one of the first organizational changes Musharraf made was to create a dedicated organization that would exclusively deal with nuclear issues. He reverted the conventional operations and acquisitions in GHQ with the military operations directorate. He merged the nuclear components of the CD Directorate with SPD and moved it to Joint Services Headquarters (JSHQ), where the nuclear operations and assets of Pakistan air force and navy were merged into one coherent command systems under whose control all scientific organizations were brought. The head of SPD was Lt. General Khalid Ahmad Kidwai, who has retained this position since December 1998 and now as a civilian sine his retirement from active duty in 2007.
In April 1999, some six months after becoming the Chief of Army Staff, General Pervez Musharraf presented a new plan to Prime Minister Nawaz Sharif for the establishment of National Command Authority (NCA). The plan was presented in a detailed briefing in GHQ, which included key cabinet ministers, bureaucracy and service chiefs, the NCA concept and organizational aspects were presented and discussed. The proposal envisaged a three tier institutional structure over the country’s nuclear weapons. The first tier constituted an the Employment Control Committee which was the apex body of decision under the Prime minister comprising five key cabinet ministers and four service chiefs; and Development Control Committee which is subordinate to Employment Control committee to implement nuclear development directive,, which was chaired by Prime minister and comprised four service chiefs and four heads of scientific organizations.
The Strategic Plans Division (SPD) which was established and already functioning by this time in JSHQ is the second tier of the NCA. SPD acts as the secretariat of the NCA. The third tier of the command system constitutes the three services’ strategic forces commands of Army, Air Force and Navy, who exercise training and administrative control of nuclear forces but the operational control of nuclear forces remains with the the NCA.
Prime Minister Sharif approved the proposal in principle but asked his foreign minister to examine it. Sharif’s skepticism resulted from his fears of the military obtaining an overarching role in national security affairs. The military has been a long-time proponent of establishing a national security council at the apex of power to ensure an institutional forum to discuss serious national issues.
As long as President Musharraf stayed in office, the President of Pakistan was the Chairman of the NCA and the prime minister was the Vice Chairman. This structure was promulgated in the NCA Ordinance on December 13, 2007.
Executive power has since returned to the prime minister, who is now the Chairman of the NCA. In February 2008, elections brought civilian government back to power. In August 2008, Musharraf resigned under pressure of impeachment from the elected parliament formally ended a prolonged transition from a hybrid system into a fully democratic parliamentary system.
For over three years since this change, Pakistan has undergone tremendous domestic tumult resulting from a series of regional crises and violent extremism, a democratic system facing multitudinous threats to its security. Meanwhile its nuclear capability and force goals have grown steadily, keeping pace with its rival India, where force modernization and strategic development in both the conventional and nuclear realms have significantly improved. Pakistan’s nuclear force posture in part has been affected since the United States gave India a lucrative nuclear deal and may soon join the elite club of nuclear supplier groups and export control regimes.
Despite tumultuous political history and a challenging security circumstances in which Pakistani nuclear program progressed; there was not any terrifying moment when there existed a danger of nation losing control of the arsenals. From the early 1970s, when the weapons program commenced it was directed from the highest political office in the country from Z A Bhutto (1971- 1977) to Zia-ul – Haq (1977- 1988) to President Ghulam Ishaq Khan (1988- 1993)
Two political transitions were especially important in which there could have been a control problem, but in each occasion the military had an organizational system to prevent any such danger, The first was immediately after sudden plane crash of President General Zia-ul- Haq when the entire military leadership vanished, but then the nuclear program came under the control of a President Ghulam Ishaq Khan who was a veteran and consistent member of the coordination committee for the nuclear program and always an insider of the program. The second occasion was when in July 1993 when President and Prime Minister both left the office after political infighting. The program them shifted to Army Headquarters, which was the most viable and robust national institution in Pakistan. Since then the political system continued to be in turmoil, but the nuclear weapons program remained fire-walled from such shocks. Though Pakistan’s civil-military relations are still under stress and unsettled and barring few critiques, the existing command and control system in the country is viewed as robust, institutional and professional, which has support across the entire political system.
The role of the COAS historically has been pivotal in Pakistani nuclear history. When Zia was both President and COAS, he did not involve the military institution in the nuclear oversight and program but only in support role. When he died, President Ghulam Ishaq Khan made the army his right hand. He asked the COAS to help coordinate and support the program on his behalf until he departed office in 1993, handing over responsibility to the Army. President Ishaq Khan never said a word after his retirement until his death, but he was never trusted the political leadership with the sensitivity of the nuclear program.
During the ten-year period of democracy, the role of prime minister on nuclear control was matter of controversy and power struggle. When the military coup occurred there was no ambiguity where the apex of power rested. It took a decade to develop and robust command system, which transited to the civilian, set up without any hiccups in 2008. Before the military take over and formulation of SPD, the non- accountability of the AQ Khan network and weak oversight resulted in the loss of control of procurement activities and illicit trade in nuclear weapons under the AQ Khan network. Several complex factors contributed to this lack of oversight and control: free national program of all bureaucratic hurdles and provide sufficient autonomy to scientific bureaucracy; created finance incentives and innovate financial means to lure in suppliers and ensure continuity of the program; allow unfettered access to procure technologies into the country by allowing need to know basis; a peculiar diffusion at the apex of political power allowed exploitation space to A Q Khan to conduct a lucrative trade in nuclear technology.
With the military in control and changed regional and international environment after 9/11, the military regime of President Musharraf instituted a tight control in unraveling the network and shaped the nuclear management on modern command and control system, robust enough to withstand political shocks and a system to deal with nuclear postures and status in peace, crises and war. Since it conducted the nuclear tests in 1998 its deterrent posture as well as command and control has been tested under regional crises and domestic violence. Above all it went through peaceful transition in 2008 for the first time in history, even though it went through violence and domestic crisis the like of which was unprecedented in its short history.