Move to C.I.A. Puts Petraeus in Conflict With Pakistan

Pakistani and American officials said that General Petraeus’s selection could further inflame relations between the two nations, which are already at one of their lowest points, with recriminations over myriad issues aired publicly like never before.

The usually secretive leader of the Pakistani Army, Gen. Ashfaq Parvez Kayani, has made little secret of his distaste for General Petraeus, calling him a political general. General Petraeus has privately expressed outrage at what American officials say is the Pakistani main spy agency’s most blatant support yet for fighters based in Pakistan who are carrying out attacks against American troops in Afghanistan.

Officials on both sides say they expect the two nations’ relationship to become increasingly adversarial as they maneuver the endgame in Afghanistan, where Pakistan and the United States have deep — and conflicting — security interests.

Repairing the frayed ties between the C.I.A. and Pakistan’s primary spy agency, the Inter-Services Intelligence Directorate, will be difficult, American officials say. “In its current form, the relationship is almost unworkable,” said Dennis C. Blair, a former American director of national intelligence. “There has to be a major restructuring. The ISI jams the C.I.A. all it wants and pays no penalties.”

One top adviser to General Petraeus sought to play down the animosity with Pakistani officials, noting that the general had regularly met with the Pakistanis for nearly three years, most recently on Monday. Still, the adviser acknowledged that with General Petraeus leading the C.I.A., “the pressure may be more strategic, deliberate and focused — to the extent that it can be.”

A Pakistani official described the mounting tensions as a game of “brinkmanship,” with both Adm. Mike Mullen, who as chairman of the Joint Chiefs of Staff has been the Obama administration’s point man on Pakistan policy, and General Kayani growing impatient because they have little to show for the many hours they have invested during more than two dozen visits over the past three years.

Admiral Mullen surprised Pakistani officials by publicly accusing the ISI of sheltering fighters from the Haqqani network, a Taliban ally that has long served as a proxy for Pakistan’s military and intelligence establishment in Afghanistan. American commanders in eastern Afghanistan say they have killed or captured more than 5,000 militants in the past year, but fighters continue to pour across the border from sanctuaries in Pakistan to Paktia, Khost and Paktika Provinces in Afghanistan.

In a private meeting here in Islamabad last week, Admiral Mullen told General Kayani that the C.I.A. would not reduce the drone strikes until Pakistan launched a military operation against the Haqqani network in Pakistan’s tribal areas, an American official said, pleas that the admiral has been making for the past two years with nothing to show for them.

Pakistan’s military and its intelligence agency are increasingly embarrassed by the United States’ drone campaign, which they publicly condemn but quietly allow. They have asked the C.I.A. to remove its personnel from Shamsi air base, about 200 miles southwest of Quetta, the capital of Baluchistan Province, where some of the drones are based, a senior American official said.

The withdrawal has not occurred but is expected soon, the official said. The drone attacks would then be flown out of Afghanistan, where some of them are already based, the official said.

There have also been sharp disagreements over a proposed code of conduct that would define what American soldiers and intelligence agents can do in Pakistani territory, a Pakistani official said. The Pakistanis have, for now, dropped the idea of such an accord, fearing that the Americans are looking for “legal cover” for intelligence operatives like Raymond A. Davis, the C.I.A. contractor who killed two Pakistanis in January, a Pakistani official said.

“The relationship between the two countries is very tense right now,” said Representative William M. Thornberry of Texas, a senior Republican on the House Armed Services Committee, who visited Pakistan last week. “And the Pakistan government fuels the anti-American public opinion to increase pressure on us.”

Newly disclosed documents obtained by WikiLeaks have also stoked tensions. One of them, from the prison at Guantánamo Bay, Cuba, lists the ISI along with numerous militant groups as allies of Al Qaeda and the Taliban, an indication of how deep American suspicions run when it comes to Pakistani intelligence. The document is undated but appears to be from 2007 or 2008.

Jane Perlez reported from Islamabad, and Eric Schmitt from Washington. Ismail Khan contributed reporting from Peshawar, Pakistan, and Scott Shane from Washington.