Numerous terrorist groups, including the Haqqani Network (HQN), Lashkar e-Tayyiba (LeT), and Jaish-e-Mohammad (JeM), continued to operate from Pakistani soil in 2016. Although LeT is banned in Pakistan, LeT's wings Jamaat-ud-Dawa (JuD) and Falah-i-Insaniat Foundation (FiF) were able to openly engage in fundraising, including in the capital. LeT's chief Hafiz Saeed (a UN-designated terrorist) continued to address large rallies, although in February 2017, Pakistan proscribed him under relevant provisions of Schedule Four of the Anti-Terrorism Act, thus severely restricting his freedom of movement. The 2015 ban on media coverage of Saeed, JuD, and FiF continued and was generally followed by broadcast and print media. The Pakistani government did not publicly reverse its December 2015 declaration that neither JuD nor FiF is banned in Pakistan, despite their listing under UN sanctions regimes, although in January 2017, Pakistan placed both organizations "under observation" pursuant to Schedule Two of the Anti-Terrorism Act. While not a ban, this allows the government to closely scrutinize the activities of both organizations. On November 11, Pakistan's National Counterterrorism Authority published its own list of banned organizations that placed JuD in a separate section for groups that are "Under Observation," but not banned. Pakistan continued military operations to eradicate terrorist safe havens in the Federally Administered Tribal Areas, although their impact on all terrorist groups was uneven.

Throughout 2016, the Government of Pakistan administered an Exit Control List intended to prevent terrorists from traveling abroad.

To combat weapons of mass destruction (WMD) trafficking, Pakistan harmonized its national control list with items controlled by the Nuclear Suppliers Group, and continued to harmonize its control lists with other multilateral regimes, such as the Missile Technology Control Regime and the Australia Group. Pakistan improved legal and regulatory cooperation, industry outreach, and nonproliferation awareness for the Strategic Export Control Division and Pakistani Customs. In addition to industry outreach, Pakistan also delivered technical trainings to licensing and enforcement officials for the proper detection, interdiction, and identification of dual-use commodities that could be used to create WMDs.

Pakistan was a constructive and active participant in the Nuclear Security Summit process and in the Global Initiative to Combat Nuclear Terrorism, and worked to strengthen its strategic trade controls, including updating its national export control list. The State Department's Export Control and Related Border Security (EXBS) Program increased the Government of Pakistan's enforcement capacity by sponsoring training for Pakistani Customs and the Strategic Export Control Division officials on how to properly identify strategic commodities of concern. These commodity identification and advanced interdiction trainings were implemented by the U.S. Department of Energy.

EXBS also sponsored regional collaboration through nonproliferation fellowships and cross-border coordination with Afghanistan through the UN Office of Drugs and Crime – World Customs Organization's Container Control Program (CCP). Under the CCP, training was provided to enhance the targeting of skills of port control unit officials at the Jalalabad border-crossing and encouraged sharing of customs data between countries.

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