The resignation of Pakistan’s President General Pervez Musharraf after nine years in power and the return of a civilian-led government in the recent presidential election have raised questions about how the nuclear security system in Pakistan will operate in a period of political transition and turmoil.

Pakistan has a moderately sized nuclear arsenal and infrastructure, but it is growing. Since 1999, under the presidency of Musharraf, Pakistan’s nuclear security processes have evolved substantially. Musharraf created the National Command Authority (NCA), which institutionalized a command-and-control mechanism over Pakistan’s nuclear weapons program. During this period, Pakistan also established a system to manage its nuclear infrastructure and strategic assets, strengthened its physical security and operational procedures, improved its export control system, and instituted a personnel reliability program. This system seems to have operated well while Musharraf, an Army general, ran the country. Questions have been raised, however, about whether the system will work smoothly when a civilian president is at the top of the command structure.

Opinions vary widely on the possibilities. For example, one foreign expert has stated that even under optimistic scenarios, “There will still be the problem that Pakistan’s nuclear capabilities have a tendency to leak elsewhere.” [1] There is also concern that if an Islamist revolution took place in Pakistan, “Iran could try to expand its axis eastward.” [2] But Pakistani experts refute these possibilities and assert that, “There is zero chance of extremists’ control over nuclear warheads.” [3] The consensus of informed expert and governmental opinion, at least in the West, appears to be that if the military remains united and cohesive and Pakistani domestic political tensions can be managed, the nuclear security system will continue to operate effectively under civilian leadership.

Nuclear Security Threat Scenarios
A number of scenarios raise concerns about the control of Pakistan’s nuclear arsenal.

• Islamist Takeover: The major challenge inside Pakistan is considered to be the growth of Islamic extremism. The Pakistani people, however, have not exhibited deep support for Islamist political parties during the last two elections. In each of the 2008 elections – the February legislative election and the September presidential election – the major coalition of Islamic parties received around just 2 percent of the vote. According to the International Crisis Group, “Poll after poll has found that if fair and free elections were held under constitutional protections and monitored by national and international observers, the result would be a moderate, pro-Western, anti-extremist government in Pakistan.”[4]
  
  
• Islamist Penetration of Key Institutions: A significant question revolves around the reliability of the Pakistani military and the employees of nuclear facilities, especially in the younger generations that are more susceptible to the lure of Islamic fundamentalism. One concern is about the changing demographics of the Pakistani military. Recently, the military has become more diverse, with Pashtuns, Sindhis, and Baluchis now represented. So far, this has not caused factionalism in the Army, but with new political leadership and growing domestic tensions this remains a concern. What remains more opaque is how the nuclear facilities in Pakistan are staffed. This concern has been exacerbated by the discoveries that the ultimate nuclear insider, A.Q. Khan, was running an international nuclear proliferation operation and that two Pakistani physicists with knowledge of the nuclear program (retired Pakistan Atomic Energy Commission scientists) had spoken with Osama Bin Laden. In the wake of Musharraf’s resignation, one senior Bush administration official referred to “steadfast efforts” by the extremist groups to infiltrate Pakistan’s nuclear laboratories. [5] While action has been instituted to improve facility security and screen personnel who work in the nuclear program more rigorously, this is an ongoing challenge.
  
  
• Political Assassination: Political assassination in Pakistan is a real concern and terrorist acts against government and domestic targets are increasing. Benazir Bhutto was killed while campaigning for the presidency in 2008 and several attempts have been made on Musharraf’s life. Should the President be killed, however, it is clear that the military would continue to maintain control of the nuclear assets because they are considered to be the crown jewels of Pakistan’s defense. [6]
  
  
• Nuclear Umbrellas and Leakage: A.Q. Khan’s covert nuclear technology proliferation network damaged Pakistan’s claims of adequate nuclear security. It is important to note, however, that most of this covert activity predated the establishment of formal command and control mechanisms. Still, questions linger about whether it could occur again. For example, a survey of more than 100 U.S. foreign policy experts by Foreign Policy magazine and the Center for American Progress, which publishes an annual terrorism index that gauges shifts in perception of threats facing the United States, found that 69 percent consider Pakistan the country most likely to transfer nuclear technology to terrorists. [7] Irrespective of the reality, this is a significant perception problem. Perhaps more important is the emerging issue of how Pakistan would react to a nuclear armed Iran. Would they spread their nuclear technology to allies to counter the Iranian bomb? Or might they extend their nuclear umbrella to cover vulnerable countries like Saudi Arabia?
  

What We Know
Most of what is known about Pakistan’s nuclear security system comes from briefings and information provided by the Strategic Plans Division (SPD). While the information is important and useful, the Pakistani military is very wary of revealing too much or allowing foreigners to get too close to the system. Independent verification of the system’s functioning and effectiveness, therefore, has not been possible to date.

The main structure for the control of Pakistan’s nuclear infrastructure is the NCA. It consists of a three-tiered structure - the Employment Control and Development Control Committees, SPD, and Services’ Strategic Forces. The NCA is governed by a 10-member committee with the President and Prime Minister serving as the Chairman and Vice Chairman, respectively. While the President and Prime Minister lead the NCA, it is the military’s SPD that is tasked with the day-to-day management of Pakistan’s strategic assets. As the Secretariat to the NCA, the SPD maintains budgetary and administrative oversight of nuclear weapons-related organizations, and oversees a security division of 10,000 personnel who are responsible for securing the nuclear infrastructure.

Pakistan can deliver its nuclear weapons either by aircraft or surface-to-surface missiles. The weapons are believed to be kept separate from their delivery systems and the nuclear cores removed from their detonators. [8] There are also assertions that the weapons may be dispersed at up to six separate locations. [9] While it is difficult to determine precisely the number of actual weapon storage sites, Pakistani officials have clearly stated that nuclear weapons have been distributed to multiple sites. Moreover, despite their disassembled status, General Khalid Kidwai, head of the SPD, has stated that the weapons could be assembled very quickly. [10]

While not originally equipped with permissive action links (PALs), which require the entry of a code before the weapon can be detonated, Pakistani officials have stated that the warheads are now fitted with this code-lock device, and General Kidwai publicly confirmed the employment of PALs in November 2006. [11] The Pakistanis have not provided details on how their PAL system works, leading to questions about the system’s operation. Given that the U.S. PAL system is designed for intact weapons, some analysts are confused, for example, as to how a PAL system would operate if the weapon’s pit is separated from the warhead. But, the Pakistanis are not likely using U.S. technology and may have designed a system that is specific to their needs and force structure. This could be a situation in which the arming sequence is operationalized once the fissile package is inserted. In addition, like other advanced nuclear weapon states, Pakistan follows a two-man rule to authenticate the codes that call for the release of the weapons. It may, in fact, be a three-man procedure in some cases.

Pakistan has also taken steps to improve the defense of its nuclear installations, whether civilian or military. Central responsibility for security and physical protection of nuclear facilities resides with the SPD. Presently, a multi-layered approach is employed for perimeter security. The inner perimeter is overseen by elements of the coordinated security division of the SPD, which operate on a permanent basis and receive special training. Certain facilities are also protected by air defense elements and are designated as no-fly zones. The outer perimeter fencing at facilities has recently been strengthened, and new technologies and electronic sensors, including CCTV cameras, have been installed. In addition, counter intelligence teams work to identify external threats to facilities. A key concern in Pakistan is the security of weapons and materials in transit. Officials are, therefore, seeking to acquire additional specialized vehicles to prevent sabotage attempts.

Like other countries, Pakistan recognizes that “nuclear security” extends beyond those facilities that house nuclear weapons. The Pakistan Nuclear Regulatory Authority (PNRA) is responsible for safety and security measures at nuclear facilities and implementing recommendations and guidance received from the International Atomic Energy Agency (IAEA). The PNRA is also responsible for the security of radioactive sources in the country, the total number of which is not clear. The PNRA claims that the amount of category 1, 2, and 3 radioactive materials is limited and once the material’s useful life is over it must be returned to the government. [12] The security of radioactive sources is ensured through periodic physical verification and regulatory inspections. In recent years, the PNRA has conducted numerous nationwide inspections of nuclear and radiation facilities, identifying weaknesses and recommending countermeasures. The PNRA has also launched an orphan sources initiative through a public awareness and education campaign.

Pakistan has signed the Container Security Initiative which provided detectors in Karachi. In addition, as part of a United States Second Line of Defense (SLD) Megaports pilot program, radiation portal monitors and non-intrusive imaging equipment were deployed, and a central alarm station manned by Pakistanis was established, at Port Qasim in southern Pakistan. Pakistan also participates in the IAEA Illicit Trafficking Database which allows countries to share information on incidents involving theft, loss, or pilferage of radiological materials.

Since 2001 the personnel system has been strengthened and reliability testing has been integrated into the nuclear establishment. The security clearance and screening of individuals for employment in the strategic organizations is now consolidated through a Personnel Reliability Program (PRP), which covers all persons working in the sensitive areas of the nuclear system. The SPD has overall approval of key personnel and also retains information on all retired personnel. Also, as the nuclear departments have grown, there is less of a sense of “family bonding” and more accountability. Any individual assigned to a strategic project or a sensitive task now undergoes a security clearance by Interservices Intelligence (ISI), Intelligence Bureau, Military Intelligence, and the SPD. This system is based on the U.S. PRP system and includes re-checks every two years or when an employee is transferred to a new program. The process includes complete background checks on family, educational career, political affiliations and inclinations.

Challenges remain, however, in controlling nuclear expertise. Pakistan has reemployed scientists with potentially sensitive expertise in other areas of the nuclear program to continue to use their knowledge. Once the system becomes more saturated and more scientists leave the program, dealing with these alumni will become more difficult. Pakistan has spoken with the United States on this issue and is exploring possibilities for employing scientists who leave the program, including retraining them in other areas. This issue needs to be addressed in greater detail in order to devise an effective and sustainable system for Pakistan.

Cooperation with the International Community
The IAEA is an important avenue for both short- and long-term nuclear security support for the safeguarded nuclear facilities in Pakistan. Pakistan is a member of the IAEA and any nuclear or radioactive material that enters into the safeguarded system comes under the supervision of the Agency, which monitors and tracks the movement of materials through the system until they are disposed.

Four of Pakistan’s nuclear facilities currently operate under IAEA safeguards: the Karachi and Chasma-1 power reactors and the Pakistan Atomic Research Reactors I and II in Rawalpindi. Several key nuclear weapons-related facilities, however, are not subject to IAEA inspections. One is the Khan Research Laboratory, which produces weapons-grade uranium. Other uranium-related facilities not under safeguards are the enrichment facilities believed to be at Golra, Sihala, and Gadwal. The Pakistani government has never officially acknowledged the existence of these facilities and it does not provide them in the list of facilities exchanged with India on January 1 every year. Plutonium-related facilities not subject to safeguards include the Khushab research reactor – which is estimated to have a capacity of about 50 megawatts, sufficient to produce enough plutonium for a few nuclear weapons per year – and New Laboratories – a plutonium reprocessing plant. [13]

The United States and Pakistan initiated a bilateral dialogue on improving nuclear security in the wake of the 9/11 attacks. The results of the discussions are sensitive, though not strictly secret, as references to the cooperation have been made in Western and Pakistani news media, other expert publications, and briefings to Pakistani parliamentarians. [14] The discussions have been conducted at the expert level and on a non-sensitive and non-intrusive basis with Pakistan insisting on clear “red lines.” The scope of the talks reportedly includes export and commodity controls, personnel reliability programs, nuclear material protection, control and accounting, transportation security, sharing of best practices, training of security personnel, and the provision of equipment. The funding level has been reported to be around $100 million. According to the Pakistani Ministry of Foreign Affairs, the cooperation has been “of a basic nature.” [15]

This cooperation does not extend to the “safety” of nuclear weapons because of limitations of U.S. law as well as Pakistan’s insistence on non-intrusiveness and on maintaining secrecy related to its nuclear weapons and their locations. Another very sensitive issue is the suggestion that the United States is engaging in contingency planning to “secure” or relocate Pakistani nuclear assets in case of a break down of order in that country. [16] This is not part of the U.S.-Pakistan nuclear security dialogue and suggestions of this course of action are met with vehement opposition from Pakistani officials.

The future of this cooperation is open to question. It was originally approved by President Musharraf, and it is not clear what the new government will do with it or if the Pakistani military wants it to continue. This ambiguous situation exists, in part, because it is not clear how much further it can be pursued without taking it in a more in-depth and politically sensitive direction. Pakistan might want to consider, however, what the next steps would look like. It has been suggested, for example, that the Pakistanis may be willing to allow a friendly party such as China to examine its security system and report back its findings on a limited and protected basis to other countries. [17] Also, in the wake of the U.S.-India nuclear cooperation agreement, Pakistan has intensified its interest in re-establishing a normal nuclear trade and cooperation relationship with the West. This is a controversial proposal but one that might be more successful if Pakistan laid additional ground work by being more open and transparent about its past activities, and accepted certain criteria that would help to move it further into the nuclear and nonproliferation mainstream. [18]

Conclusion
Pakistani nuclear security is a serious international concern. The nation has a moderately sized, but growing, arsenal, and the system controlling it has been strengthened but remains opaque. In general, government officials and outside experts consider the improvements made by Musharraf to have been a significant improvement over the previous system of control. Still, concerns remain. The political transition from Musharraf to Asif Ali Zardari is occurring in a period of political turmoil. The installation of a civilian president at the head of the NCA could cause tensions with the military, which controls the nuclear installations and assets on a day-to-day basis. There could be infighting and struggles among the three top positions of the NCA – the President, Prime Minister, and the military commander. Moreover, regional developments and tensions could challenge the security situation, particularly if tensions with India rise or if Iran becomes a declared nuclear weapon state.

All of this uncertainty places pressure on the Pakistani government to consider how to provide additional measures of assurance to the international community about its nuclear security and intentions.

Kenneth N. Luongo – Partnership for Global Security