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Nukes, terrorists, intel gaps: U.S. ‘black budget’ shows extent of distrust toward Pakistan

by Barton Gellman

The Washington Post

The $52.6 billion U.S. intelligence arsenal is aimed mainly at unambiguous adversaries, including al-Qaida, North Korea and Iran. But top-secret budget documents reveal an equally intense focus on one purported ally: Pakistan.

No other nation draws as much scrutiny across so many categories of national security concern.

A 178-page summary of the U.S. intelligence community’s “black budget” shows that the United States has ramped up its surveillance of Pakistan’s nuclear arms, cites previously undisclosed concerns about biological and chemical sites there, and details efforts to assess the loyalties of counterterrorism sources recruited by the CIA.

Pakistan appears at the top of charts listing critical U.S. intelligence gaps. It is named as a target of newly formed analytic cells. And fears about the security of its nuclear program are so pervasive that a budget section on containing the spread of illicit weapons divides the world into two categories: Pakistan and everybody else.

The disclosures — based on documents provided to The Washington Post by former intelligence contractor Edward Snowden — expose broad new levels of U.S. distrust in an already unsteady security partnership with Pakistan, a politically unstable country that faces rising Islamist militancy. They also reveal a more expansive effort to gather intelligence on Pakistan than U.S. officials have ever disclosed.

The United States has delivered nearly $26 billion in aid to Pakistan over the past 12 years, aimed at stabilizing the country and ensuring its cooperation in counterterrorism efforts. But with Osama bin Laden dead and al-Qaida degraded, U.S. spy agencies appear to be shifting their attention to dangers that have emerged beyond the patch of Pakistani territory patrolled by CIA drones.

“If the Americans are expanding their surveillance capabilities, it can only mean one thing,” said Husain Haqqani, who until 2011 served as Pakistan’s ambassador to the United States. “The mistrust now exceeds the trust.”

Beyond the budget files, other classified documents provided to The Washington Post expose fresh allegations of systemic human rights abuses in Pakistan. U.S. spy agencies reported that high-ranking Pakistani military and intelligence officials had been aware of — and possibly ordered — an extensive campaign of extrajudicial killings targeting militants and other adversaries.

Public disclosure of those reports, based on communications intercepts from 2010 to 2012 and other intelligence, could have forced the Obama administration to sever aid to the Pakistani armed forces because of a U.S. law that prohibits military assistance to human rights abusers. But the documents indicate that administration officials decided not to press the issue in order to preserve an already frayed relationship with the Pakistanis.

In a statement, a spokeswoman for the National Security Council said the United States is “committed to a long-term partnership with Pakistan, and we remain fully engaged in building a relationship that is based on mutual interests and mutual respect.”

“We have an ongoing strategic dialogue that addresses in a realistic fashion many of the key issues between us, from border management to counterterrorism, from nuclear security to promoting trade and investment,” said the spokeswoman, Caitlin Hayden. “The United States and Pakistan share a strategic interest in combating the challenging security issues in Pakistan, and we continue to work closely with Pakistan’s professional and dedicated security forces to do so.”

The Post agreed to withhold some details from the budget documents after consultations with U.S. officials, who expressed concern about jeopardizing ongoing operations and sources.

A spokesman for the Pakistani Embassy in Washington did not respond to a request for comment.

Stark assessments of Pakistan contained in the budget files seem at odds with the signals that U.S. officials have conveyed in public, partly to avoid fanning Pakistani suspicions that the United States is laying contingency plans to swoop in and seize control of the country’s nuclear complex.

When Director of National Intelligence James Clapper was asked during congressional testimony last year whether Pakistan had appropriate safeguards for its nuclear program, he replied, “I’m reasonably confident they do.” Facing a similar question this year, Clapper declined to discuss the matter in open session.

But the classified budget overview he signed and submitted for fiscal 2013 warned that “knowledge of the security of Pakistan’s nuclear weapons and associated material encompassed one of the most critical set of . . . intelligence gaps.” Those blind spots were especially worrisome, the document said, “given the political instability, terrorist threat and expanding inventory [of nuclear weapons] in that country.”

The budget documents do not break down expenditures by country or estimate how much the U.S. government spends to spy on Pakistan. But the nation is at the center of two categories — counterterrorism and counter-proliferation — that dominate the black budget.

In their proposal for fiscal 2013, which ends Sept. 30, U.S. spy agencies sought $16.6 billion to fight al-Qaida and other terrorist groups, and asked for $6.86 billion to counter the spread of nuclear, biological and chemical weapons. Together, the two categories accounted for nearly half of the U.S. intelligence community’s budget request for this year.

Detailed spreadsheets contain dozens of line items that correspond to operations in Pakistan. The CIA, for example, was scheduled to spend $2.6 billion on “covert action” programs around the world. Among the most expensive, according to current and former U.S. intelligence officials, is the armed drone campaign against al-Qaida fighters and other militants in Pakistan’s tribal belt.

U.S. intelligence analysts “produced hundreds of detailed and timely reports on shipments and pending deliveries of suspect cargoes” to Pakistan, Syria and Iran. Multiple U.S. agencies exploited the massive American security presence in Afghanistan — including a string of CIA bases and NSA listening posts along the border mainly focused on militants — for broader intelligence on Pakistan.

After years of diplomatic conflict, significant sources of tension between the United States and Pakistan have begun to subside.

The pace of CIA drone strikes has plunged, and two years have passed since U.S. leaders infuriated Islamabad by ordering the secret raid inside Pakistani territory that killed bin Laden.

Although Pakistani anger has abated, Haqqani said the fallout from the raid had broader consequences than widely understood.

“The discovery of bin Laden [in Pakistan] made the Americans think that the Pakistani state’s ability to know what happens within the country is a lot less than had been assumed,” said Haqqani, an international relations professor at Boston University.

That realization may have ratcheted up a long-standing source of concern: Pakistan’s ability to safeguard its nuclear materials and components.

U.S. intelligence agencies are focused on two particularly worrisome scenarios: the possibility that Pakistan’s nuclear facilities might come under attack by Islamist militants, as its army headquarters in Rawalpindi did in 2009, and even greater concern that Islamist militants might have penetrated the ranks of Pakistan’s military or intelligence services, putting them in a position to launch an insider attack or smuggle out nuclear material.

Pakistan has dozens of laboratories and production and storage sites scattered across the country. After developing warheads with highly enriched uranium, it has more recently tried to do the same with more-powerful and compact plutonium. The country is estimated to have as many as 120 nuclear weapons, and the budget documents indicate that U.S. intelligence agencies suspect that Pakistan is still adding to that stockpile.

Little is known about how it moves materials among its facilities, an area that experts have cited as a potential vulnerability.

“Nobody knows how they truly do it,” said Feroz Khan, a retired Pakistani military officer and director of arms control who lectures at the U.S. Naval Postgraduate School in Monterey, Calif. “Vehicles move in a stealthy manner and move with security. But it’s not clear whether the cores are moved to the warheads or the warheads are moved to the core locations.”

Concerns persist that extremists could seize components of the stockpile or trigger a war with neighboring India. Pakistan also has a track record of exporting nuclear technology to countries that are on Washington’s blacklist.

Pakistan has accepted some security training from the CIA, but U.S. export restrictions and Pakistani suspicions have prevented the two countries from sharing the most sophisticated technology for safeguarding nuclear components.

U.S. anxiety over Pakistan’s nuclear program appears to be driven more by uncertainty about how it is run than specific intelligence indicating that its systems are vulnerable, according to the budget documents.

A lengthy section on counter-proliferation starts with a single goal: “Make Quantitative and Qualitative Progress against Pakistan Nuclear Gaps.” A table indicates that U.S. spy agencies have identified at least six areas in which their understanding of Pakistan’s weapons programs is deficient.

U.S. agencies reported gaining valuable information through “extensive efforts to increase understanding of the transfer and storage of the associated materials.”

The budget describes the creation of a Pakistan WMD Analysis Cell to track movements of nuclear materials. Agencies, including the CIA and the Defense Department, were able “to develop and deploy a new compartmented collection capability” that delivered a “more comprehensive understanding of strategic weapons security in Pakistan.”

Even so, “the number of gaps associated with Pakistani nuclear security remains the same,” the document said, and “the questions associated with this intractable target are more complex.”

The budget documents indicate that U.S. intelligence agencies are also focused on the security of the nuclear program in India, Pakistan’s arch-rival.

U.S. surveillance of Pakistan extends far beyond its nuclear program. There are several references in the black budget to expanding U.S. scrutiny of chemical and biological laboratories. The country is not thought to be running a rogue chemical or biological weapons program, but U.S. intelligence officials fear that Islamists could seize materials from government-run laboratories.

Even American interdiction operations targeting other countries have stumbled into connections with Pakistan. In one case, a U.S. effort to block an Iranian shipment through a Turkish port “proved to be even more successful when aluminum powder destined for Pakistan was also discovered and detained,” according to the documents. Aluminum powder can be used to increase the power of explosives.

The budget documents don’t disclose CIA payments to its Pakistani counterpart, the Inter-Services Intelligence directorate, or ISI, which former officials said has totaled tens of millions of dollars. The documents do show that the CIA has developed sophisticated means of assessing the loyalties of informants who have helped the agency find al-Qaida leaders in Pakistan’s tribal region.

Those measures, which The Post has agreed not to disclose, have allowed the CIA to “gain confidence in each asset’s authenticity, reliability and freedom from hostile control.”

Other classified documents given to The Post by Snowden reveal that U.S. spy agencies for years reported that senior Pakistani military and intelligence leaders were orchestrating a wave of extrajudicial killings of terrorism suspects and other militants.

In July 2011, an assessment of communications intercepts and other intelligence by the NSA concluded that the Pakistani military and intelligence services had continued over the preceding 16 months a pattern of lethally targeting perceived enemies without trial or due process. The killings, according to the NSA, occurred “with the knowledge, if not consent, of senior officers.”

The NSA cited two senior Pakistani officials who “apparently ordered some of the killings or were at least aware of them,” read a summary of the top-secret NSA report, titled, “Pakistan/Human Rights: Extrajudicial Killings Conducted With Consent of Senior Intelligence Officials.”

The report summary did not provide an estimate of how many people had been killed or their identities. But it generally described the targets as people whom the Pakistani security forces viewed as “undeniably linked to terrorist activity” or responsible for attacks on Pakistan’s armed forces.

The killings “seemed to serve the purpose of dispensing what the military considered swift justice,” the intelligence assessment stated. Pakistani authorities “were conscious of not arousing suspicions. The number of victims at a given time tended to be very small. Furthermore, the military took care to make the deaths seem to occur in the course of counterinsurgency operations, from natural causes, or as the result of personal vendettas.”

Although Pakistan has been engaged for years in open warfare with Taliban factions and other domestic insurgents, the NSA placed the extrajudicial killings in a much darker category. Pakistani police forces “were reluctant to carry out the killings,” the report said.

The NSA compiled its report shortly after the public exposure of other alleged Pakistani atrocities.

In June 2010, the Human Rights Commission of Pakistan charged that Pakistani forces had carried out more than 280 summary executions during an offensive against Taliban fighters and other militants, mostly in the Swat Valley. Five months later, a video surfaced on the Internet showing Pakistani soldiers executing six blindfolded men with their hands tied behind their backs.

An international outcry over the latter incident prompted the Obama administration to withhold aid — but only to a handful of low-level Pakistani Army units thought to have been involved in such incidents.

At the time, Pakistani officials dismissed the video and other reports of summary executions as Taliban propaganda, but they later reversed course and launched an internal investigation. Pakistan’s military leaders insisted publicly that they had zero tolerance for such incidents.

It was not the first time that U.S. officials sought to keep evidence of Pakistani human rights abuses out of the public eye.

A classified diplomatic cable, sent from the U.S. Embassy in Islamabad to officials in Washington in September 2009, also raised concern about the extrajudicial killings of militants by Pakistani Army units. But the cable — originally released in 2010 by the anti-secrecy group WikiLeaks — advised against public disclosure of the incidents, saying it was more important to maintain support for the Pakistani armed forces.

U.S. intelligence officials have kept quiet about other signs of human rights abuses by the Pakistani military, even though their classified reporting on the subject underscores persistent concerns.

In September 2011, the summary of a top-secret report from a Defense Intelligence Agency task force cited the “systemic practice” of unlawful killings by Pakistani security forces in the tribal regions of western Pakistan.

Pakistan had recently passed a law allowing the military to detain insurgents indefinitely and make it easier to convict them in civilian courts. But the DIA concluded that because extrajudicial killings were “condoned by senior officials” in Pakistan’s security establishment, the new law was unlikely to significantly reduce the number of deaths.

Other U.S. intelligence documents indicate that Pakistani officials weren’t targeting just suspected insurgents.

In May 2012, U.S. intelligence agencies discovered evidence of Pakistani officers plotting to “eliminate” a prominent human rights activist, Asma Jahangir, according to the summary of a top-secret DIA report. Jahangir had been a leading public critic of the ISI for years.

The DIA report did not identify which officers were plotting to kill Jahangir, but it said the plan “included either tasking militants to kill her in India or tasking militants or criminals to kill her in Pakistan.”

The U.S. agency said it did not know whether the ISI had given approval for the plot to proceed. Although the report speculated that the ISI was motivated to kill Jahangir “to quiet public criticism of the military,” the DIA noted that such a plot “would result in international and domestic backlash as ISI is already under significant criticism for intimidation and extra-judicial killings.”

News of the alleged plot became public a few weeks later when Jahangir gave a round of interviews to journalists, revealing that she had learned that Pakistani intelligence officials had marked her for death. The plot was never carried out.

  • Tooba mansoor

    USA should stop poking its nose into everyone’s matter. Pakistan is a responsible state and pursuing its nuclear weapon program in a safe way. International community has also claimed that Pakistan’s nuclear weapons are safe and secured. USA is not a reliable state. It has always treated Pakistan discriminatingly and favouring India. USA doesn’t go for mutual interests rather for self interest.

  • Sandy

    Pakistan has institutionalised highly-secured systems, which has been improved gradually to thwart internal and external security challenges to its nuclear infrastructure and arsenals, since the very beginning of the nuclear weapons programme. Pakistan’s assessment of nuclear weapons potentially falling in the hands of religious terrorists is incorrect. yeah in South Asia biggest threat to nuclear securtiy is the Inidan nuclear security. There are more then 267 case resgistered in India of Uranium theft then the mastrius killing of Indian nuclear scientist. And more over the Hindu Extremists.

    Ashwin Kumar writes that “the safety record in India’s nuclear facilities reveals poorpractices and routine accidents”. we never thought why Pakistan needed to develop nuclear weapons???

  • Nehaan

    Amazingly, what a dichotomy! US top/ front line ally in its blind voyage of
    GWOT turned to be as a state of top level of distrustful entity. If this is a
    case, why so much huge amount of US budget is been spend on this country with the
    big label of USAID. This is an ever asking question in the mind of every American that if
    Pakistan is not a trust worthy ally than why our country spend so much blindly
    which in return just give us back a strong wave of anti-Americanism. It’s more
    than a decade of GWOT fought by our troops in Afghanistan. Not a single day has
    passed which does not reveal that American and Pakistani troops work together
    to combat terrorism. With GWOT, there is always Pakistan to give guidance and
    coordination in culminating terrorist across its border in Afghanistan. Unable to
    understand, that American Army is so fully equipped with latest technology of
    war fighting but find difficulties to stand against the common Afghan people.
    For this, they seek a support from its very distrustful ally Pakistan to stand
    its position and presence in other’s territory. If it encompasses such a danger
    and distrust; than why the US administration openly seeks the hand of
    cooperation from Pakistan in post 9/11 time period. It seemed that GWOT can’t
    be possible without the active support of Pakistan.

  • kir chovo

    What an irony, US on one hand considers Pakistan as frontline
    states in war against terrorism, on the other hand US has kept a counter check
    on Pakistan’s nuclear program. Pakistan has lost more than 50000 lives during
    war US-led war on terrorism. This is only tangible loss we mention most of the
    time. we never mentioned greatest losses which are intangible such as nations
    moral, continuous troops engagement, social anarchy etc. US must be shameful
    for spying of its friends.

  • Nehaan

    Since the creation of Pakistan,
    it seeks US cooperation on many fronts till today. But what it gets nothing
    just a long history of betrayal from the world’s super power. Being in an environment
    where one is blessed with an ever threatening big neighbor, the issue of
    survival and security is questionable as it is evident with number of wars and conflicts.
    For the sake of its territorial integrity and deter its big conventional
    military adversary, it directed its national security under the umbrella of
    nuclear weapons. Nuclear weapons are not merely the weapons in Pakistani case,
    it is assurance of its very survival of the state. Pakistan is very specific that
    it develops its nukes to have deterrence from its neighbors. Contrastingly, US
    works hand in hand in combating terrorism with Pakistan but when the things
    comes to nuclear cooperation it pulls back its hand and devoted to India. What does
    it mean? Is the America wants to made India over dominating against Pakistan
    with nuclear technology. When Pakistan asks it completely refuses. US know this
    fact very clearly this advancement shatters the strategic balance of the region. US supports to India made US so distrustful in
    counter proliferation in the world. It triggers proliferation not give
    stability. US itself a proliferator despite of actively voiced against
    proliferation. How can US be trusted in counter proliferation efforts?

  • Mania

    It should be admitted that the world
    goes into chaos, ambiguity and non-directional destination after the 9/11. More
    than after a decade what are the gains and losses is a big question. Like the ancient
    times, when the kings have nothing to do they get busy in the war. Same that
    happens with the America. In addition, it chose the South Asian region which
    fulfills its instinct of containment. And its distinct policies towards
    Pakistan and India simultaneously are an answer. The deficiencies of its own
    intelligence is tried to be covered under the Pakistan nukes. It is the failure
    of its own very administration that terrorism has not yet been removed with
    lots of loss. Likewise, it is very own Snowden no one else. America has this
    habit to cover its own failures by highlighting
    and diverting attentions on others.

  • Ahsan Ali

    Sadly the report is all about conspiracy and it also shows that US is ramping up the funding of agencies to create cells against Pakistan nuclear program, weapons security systems, chemical and biological laboratories. Director of National Intelligence James R. Clapper Jr. himself confirm that Pakistan weapons and nuclear programs is the safest in comparison to all the nuclear states. Pakistan has made clear this thousand times that its nuclear program is for peaceful purpose as well to deter the hegemony of its adversaries. Pakistan is working on developing agriculture variety, medical radioisotopes, civil, environment, and biotechnology and energy production on the basis of its advanced nuclear technology. Pakistan Institute of Nuclear Science and Technology (PINSTECH) is playing key role in developing capacity building, hundreds of scholars and scientists have been trained to understand the complexity of nuclear matter. Pakistan National Command Authority has developed proper security divisions which have more than 20,000 trained manpower and soldiers, which are fully equipped and far superior to the terrorist. The report it self declares that they is no information about Pakistan’s nuclear safety and security because it has the most efficient system, which is hard to penetrate. This shows the competency of Pakistan’s intelligence perfection and failure of US intelligence.

  • kir chovo

    Soon after 9/11, US made a comprehensive plan to keep eye on
    all kind of developments around the globe. For that purpose state government
    created separate budget of $ 52.6billion. this huge amount was utilized in
    various ways to get right information. The allocated budget was utilized in
    spying , cyber-attacks, task forces, technological equipment’s and many other
    fields. But unfortunately US kept secret eye on even its friends such as Pakistan.
    US monitored Pakistan’s nuclear program and cites of nukes, and their
    maneuvering inside the state. Even Pakistan was called as intractable target in
    secret documents. Though, Pakistan has been serving as frontline state in war
    against terrorism since 2001 but US has deceived Pakistan by spying not only
    its nuclear program but other sensitive organizations too. This illegitimate act by US will be major blow
    for pak-US relations and Pakistani government will put forward this critical
    issue.

  • Mahin Ghobad

    US want to surround another Islamic state and is against nuclear capability like Iran, It is no doubt that Russian, Chinese, Iran and Pakistan are hard targets. US will not be able to penetrate intelligence for it’s and Israel’s dark ambitions. Nevertheless if US is concerned about nuclear proliferation it should ask Israel to declare its nuclear program, in fact shut down the nuclear program.