THE $52.6 billion US intelligence arsenal is aimed mainly at unambiguous adversaries, including Al Qaeda, 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 US 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 US intelligence gaps. It is named as a target of newly formed analytic cells. And fears about the security of its nuclear programme 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 US 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 US officials have disclosed.

The United States has delivered nearly $26 billion in aid to Pakistan over the past 12 years, aimed at stabilising the country and ensuring its cooperation in counterterrorism efforts. But with Osama bin Laden dead and Al Qaeda degraded, US 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 Post expose fresh allegations of systemic human rights abuses in Pakistan. US 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 US 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 US 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.

Critical ‘intelligence gaps’

Stark assessments of Pakistan contained in the budget files seem at odds with the signals that US 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 R. Clapper Jr. was asked during congressional testimony last year whether Pakistan had appropriate safeguards for its nuclear programme, 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.

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

In their proposal for fiscal 2013, which ends Sept 30, US spy agencies sought $16.6 billion to fight Al Qaeda 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 US 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” programmes around the world. Among the most expensive, according to current and former US intelligence officials, is the armed drone campaign against Al Qaeda fighters and other militants in Pakistan’s tribal belt.

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

Anxiety over nuclear programme

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 US 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, who is an international-relations professor at Boston University. That realisation may have ratcheted up a long-standing source of concern: Pakistan’s ability to safeguard its nuclear materials and components.

US 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 US intelligence agencies suspect that Pakistan is 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 US 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 neighbouring 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 US export restrictions and Pakistani suspicions have prevented the two countries from sharing the most sophisticated technology for safeguarding nuclear components.

US anxiety over Pakistan’s nuclear programme 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 US spy agencies have identified at least six areas in which their understanding of Pakistan’s weapons programmes is deficient.

US 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 Defence 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 US intelligence agencies are also focused on the security of the nuclear programme in India, Pakistan’s arch-rival.

Other fields under scrutiny

US surveillance of Pakistan extends far beyond its nuclear programme. There are several references in the black budget to expanding US scrutiny of chemical and biological laboratories. The country is not thought to be running a rogue chemical or biological weapons programme, but US 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 US 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 totalled 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 Qaeda 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.”

Extrajudicial killings

Other classified documents given to The Post by Snowden reveal that US 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.

Human rights abuses

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

A classified diplomatic cable, sent from the US 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.

US 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 US intelligence documents indicate that Pakistani officials weren’t targeting just suspected insurgents Plot to kill Asma JahangirIn May 2012, US 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 US 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.

By arrangement with the Washington Post

Julie Tate contributed to this report.