This article is by Jane Perlez, David E. Sanger and Eric Schmitt.
ISLAMABAD, Pakistan -- Less than a month after President Obama testily assured reporters in 2009 that Pakistan's nuclear materials "will remain out of militant hands," his ambassador here sent a secret message to Washington suggesting that she remained deeply worried.
The ambassador's concern was a stockpile of highly enriched uranium, sitting for years near an aging research nuclear reactor in Pakistan. There was enough to build several "dirty bombs" or, in skilled hands, possibly enough for an actual nuclear bomb.
In the cable, dated May 27, 2009, the ambassador, Anne W. Patterson, reported that the Pakistani government was yet again dragging its feet on an agreement reached two years earlier to have the United States remove the material.
She wrote to senior American officials that the Pakistani government had concluded that "the 'sensational' international and local media coverage of Pakistan's nuclear weapons made it impossible to proceed at this time." A senior Pakistani official, she said, warned that if word leaked out that Americans were helping remove the fuel, the local press would certainly "portray it as the United States taking Pakistan's nuclear weapons."
The fuel is still there.
It may be the most unnerving evidence of the complex relationship -- sometimes cooperative, often confrontational, always wary -- between America and Pakistan nearly 10 years into the American-led war in Afghanistan. The cables, obtained by WikiLeaks and made available to a number of news organizations, make it clear that underneath public reassurances lie deep clashes over strategic goals on issues like Pakistan's support for the Afghan Taliban and tolerance of Al Qaeda, and Washington's warmer relations with India, Pakistan's archenemy.
Written from the American Embassy in Islamabad, the cables reveal American maneuvering as diplomats try to support an unpopular elected government that is more sympathetic to American aims than is the real power in Pakistan, the army and intelligence agency so crucial to the fight against militants. The cables show just how weak the civilian government is: President Asif Ali Zardari told Vice President Joseph R. Biden Jr. that he worried that the military might "take me out."
Frustration at American inability to persuade the Pakistani Army and intelligence agency to stop supporting the Afghan Taliban and other militants runs through the reports of meetings between American and Pakistani officials.
That frustration preoccupied the Bush administration and became an issue for the incoming Obama administration, the cables document, during a trip in January 2009 that Mr. Biden made to Pakistan 11 days before he was sworn in. In a meeting with Gen. Ashfaq Parvez Kayani, the army chief of staff, Mr. Biden asked several times whether Pakistan and the United States "had the same enemy as we move forward."
"The United States needs to be able to make an objective assessment of Pakistan's part of the bargain," Mr. Biden said, according to a Feb. 6, 2009, cable.
General Kayani tried to reassure him, saying, "We are on the same page in Afghanistan, but there might be different tactics." Mr. Biden replied that "results" would test that.
The cables reveal at least one example of increased cooperation, previously undisclosed, under the Obama administration. Last fall, the Pakistani Army secretly allowed 12 American Special Operations soldiers to deploy with Pakistani troops in the violent tribal areas near the Afghan border.
The Americans were forbidden to conduct combat missions. Even though their numbers were small, their presence at army headquarters in Bajaur, South Waziristan and North Waziristan was a "sea change in thinking," the embassy reported.
The embassy added its usual caution: The deployments must be kept secret or the "Pakistani military will likely stop making requests for such assistance."
Within the past year, however, Pakistan and the United States have gingerly started to publicly acknowledge the role of American field advisers. Lt. Col. Michael Shavers, an American military spokesman in Islamabad, said in a statement that "at the request of the Pakistanis," small teams of Special Operations forces "move to various locations with their Pakistani military counterparts throughout Pakistan."
Moreover, last week in a report to Congress on operations in Afghanistan, the Pentagon said that the Pakistani Army had also accepted American and coalition advisers in Quetta.
The cables do not deal with the sharp increase under Mr. Obama in drone attacks against Al Qaeda and the Taliban in the tribal areas with Pakistan's tacit approval. That is because the cables are not classified at the highest levels.
A Deep Skepticism
Over all, though, the cables portray deep skepticism that Pakistan will ever cooperate fully in fighting the full panoply of extremist groups. This is partly because Pakistan sees some of the strongest militant groups as insurance for the inevitable day that the United States military withdraws from Afghanistan -- and Pakistan wants to exert maximum influence inside Afghanistan and against Indian intervention.
Indeed, the consul general in Peshawar wrote in 2008 that she believed that some members of the Haqqani network -- one of the most lethal groups attacking American and Afghan soldiers -- had left North Waziristan to escape drone strikes. Some family members, she wrote, relocated south of Peshawar; others lived in Rawalpindi, where senior Pakistani military officials also live.
In one cable, Ms. Patterson, a veteran diplomat who left Islamabad in October after a three-year stint as ambassador, said more money and military assistance would not be persuasive. "There is no chance that Pakistan will view enhanced assistance levels in any field as sufficient compensation for abandoning support for these groups, which it sees as an important part of its national security apparatus against India."
In a rare tone of dissent with Washington, she said Pakistan would only dig in deeper if America continued to improve ties with India, which she said "feeds Pakistani establishment paranoia and pushes them closer to both Afghan and Kashmir focused terrorist groups."
The groups Ms. Patterson referred to were almost certainly the Haqqani network of the Afghan Taliban and Lashkar-e-Taiba, a group financed by Pakistan in the 1990s to fight India in Kashmir that is accused of the 2008 terrorist attacks in Mumbai, India.
The highly enriched uranium that Ms. Patterson wanted removed from the research reactor came from the United States in the mid-1960s. In those days, under the Atoms for Peace program, little thought was given to proliferation, and Pakistan seemed too poor and backward to join the nuclear race.
But by May 2009, all that had changed, and her terse cable to the State and Defense Departments, among others, touched every nerve in the fraught relationship: mutual mistrust, the safety of the world's fastest-growing nuclear arsenal, broken promises and a pervasive fear that any talk about Pakistan's vulnerability would end whatever cooperation existed.
The reactor had been converted to use low-enriched uranium, well below bomb grade, in 1990, according to the International Atomic Energy Agency, or I.A.E.A. But the bomb-grade uranium had never been returned to the United States and remains in storage nearby. Ms. Patterson's cable noted that Pakistan had "agreed in principle to the fuel removal in 2007."
But time and again the Pakistanis balked, and she reported that an interagency group within the Pakistani government had decided to cancel a visit by American technical experts to get the fuel out of the country. She concluded that "it is clear that the negative media attention has begun to hamper U.S. efforts to improve Pakistan's nuclear security and nonproliferation practices."
Any progress, she suggested, would have to await a "more conducive" political climate.
On Monday, Pakistan's Foreign Affairs Ministry issued a statement confirming that "the US suggestion to have the fuel transferred was plainly refused by Pakistan." It said that the United States had provided the fuel but did not mention that, under the terms of such transfers, the United States retained the right to have the spent fuel returned.
The ambassador's comments help explain why Mr. Obama and his aides have expressed confidence in Pakistan's nuclear security when asked in public. But at the beginning of the administration's review of its Afghanistan and Pakistan strategy, a highly classified intelligence report delivered to Mr. Obama said that while Pakistan's weapons were well secured, there was deep, continuing concern about "insider access," meaning elements in the military or intelligence services.
In fact, Ms. Patterson, in a Feb. 4, 2009, cable, wrote that "our major concern is not having an Islamic militant steal an entire weapon but rather the chance someone working in GOP [government of Pakistan] facilities could gradually smuggle enough material out to eventually make a weapon."
Mr. Obama's review concluded by determining that there were two "vital" American interests in the region. One was defeating Al Qaeda. The second, not previously reported, was making sure terrorists could never gain access to Pakistan's nuclear program. That goal was classified, to keep from angering Islamabad.
Asked about the status of the fuel at the research reactor, Damien LaVera, a spokesman for the National Nuclear Security Administration of the Energy Department, said, "The United States supplied Pakistan with fuel for a research reactor decades ago for the purpose of producing medical isotopes and scientific research." Implicitly acknowledging that the material remains there, Mr. LaVera said "the fuel is under I.A.E.A. safeguards and has not been part of Pakistan's nuclear weapons program."
One secret cable offers another glimpse into another element of the nuclear gamesmanship between the United States and its Pakistani allies: Even while American officials were trying to persuade Pakistani officials to give up nuclear material, they were quietly seeking to block Pakistan from trying to buy material that would help it produce tritium, the crucial ingredient needed to increase the power of nuclear weapons.
After providing specific details of the proposed sale, a Dec. 12, 2008, secret cable to the American Embassy in Singapore, seeking help to stop a transaction that was about to take place, concluded, "We would have great concern over Pakistan's potential use of tritium to advance its nuclear weapons program."
Reports of Army Abuses
The cables also reveal that the American Embassy had received credible reports of extrajudicial killings of prisoners by the Pakistani Army more than a year before the Obama administration publicly acknowledged the problem and before a video that is said to show such killings surfaced on the Internet.
The killings are another source of tension, complicated by American pressure on Pakistan to be more aggressive in confronting militants on its own soil.
In a Sept. 10, 2009, cable labeled "secret/noforn," meaning that it was too delicate to be shared with foreign governments, the embassy confronted allegations of human rights abuses in the Swat Valley and the tribal areas since the Pakistani Army had begun fighting the Taliban a few months earlier.
While carefully worded, the cable left little doubt about what was going on. It spoke of a "growing body of evidence" that gave credence to the allegations.
"The crux of the problem appears to center on the treatment of terrorists detained in battlefield operations and have focused on the extrajudicial killing of some detainees," the cable said. "The detainees involved were in the custody of Frontier Corps or Pakistan army units." The Frontier Corps is a paramilitary force partly financed by the United States to fight the insurgents.
The Pakistani Army was holding as many as 5,000 "terrorist detainees," the cable said, about twice as many as the army had acknowledged.
Concerned that the United States should not offend the Pakistani Army, the cable stressed that any talk of the killings must be kept out of the press.
"Post advises that we avoid comment on these incidents to the extent possible and that efforts remain focused on dialogue and the assistance strategy," the ambassador wrote. This September, however, the issue exploded into public view when a video emerged showing Pakistani soldiers executing six unarmed young men in civilian clothes. In October, the Obama administration suspended financing to half a dozen Pakistani Army units believed to have killed civilians or unarmed prisoners.
The cables verge on gossipy, as diplomats strained to understand the personalities behind the fractious Pakistani government, and particularly two men: General Kayani and President Zardari.
Often, the United States finds that Mr. Zardari, the accidental leader after the assassination of his wife, Benazir Bhutto, is sympathetic to American goals -- stiff sanctions on terrorist financing, the closing down of terrorist training camps -- but lacks the power to fulfill his promises against resistance from the military and intelligence agencies.
Mr. Zardari's chief antagonist, General Kayani, emerges as a stubborn guarantor of what he sees as Pakistan's national interest, an army chief who meddles in civilian politics but stops short of overturning the elected order.
Early in the Obama administration, General Kayani made clear a condition for improved relations. As the director general of the Directorate for Inter-Services Intelligence, or ISI, from 2004 to 2007, he did not want a "reckoning with the past," said a cable in 2009 introducing him to the new administration.
"Kayani will want to hear that the United States has turned the page on past ISI operations," it said. General Kayani was probably referring to the peace accords with the Taliban from 2004 to 2007 that resulted in the strengthening of the militants.
If the general seems confidently in charge, the cables portray Mr. Zardari as a man not fully aware of his weakness.
At one point he said he would not object if Abdul Qadeer Khan, revered in Pakistan as the father of its nuclear weapons program, were interviewed by the International Atomic Energy Agency but tacitly acknowledged that he was powerless to make that happen.
Mr. Zardari, who spent 11 years in prison on ultimately unproved corruption charges, feared for his position and possibly -- the wording is ambiguous -- his life: the cables reveal that Vice President Biden told Prime Minister Gordon Brown of Britain in March 2009 that Mr. Zardari had told him that the "ISI director and Kayani will take me out."
His suspicions were not groundless. In March 2009, a period of political turmoil, General Kayani told the ambassador that he "might, however reluctantly," pressure Mr. Zardari to resign and, the cable added, presumably leave Pakistan. He mentioned the leader of a third political party, Asfandyar Wali Khan, as a possible replacement.
"Kayani made it clear regardless how much he disliked Zardari he distrusted Nawaz even more," the ambassador wrote, a reference to Nawaz Sharif, a former prime minister.
By 2010, after many sessions with Mr. Zardari, Ms. Patterson had revised the guarded optimism that characterized her early cables about Mr. Zardari.
"Pakistan's civilian government remains weak, ineffectual and corrupt," she wrote on Feb. 22, 2010, the eve of a visit by the F.B.I. director, Robert S. Mueller III. "Domestic politics is dominated by uncertainty about the fate of President Zardari."
That assessment holds more than eight months later, even as Mr. Obama in October extended an invitation to the Mr. Zardari leader to visit the White House next year, as the leader of a nation that holds a key to peace in Afghanistan but appears too divided and mistrustful to turn it for the Americans.
This article originally appeared in The New York Times .