http://www.nytimes.com/2011/04/29/world/29petraeus.html

April 28, 2011

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

By JANE PERLEZ and ERIC SCHMITT

ISLAMABAD, Pakistan -- The appointment of Gen. David H. Petraeus as director of the Central Intelligence Agency puts him more squarely than ever in conflict with Pakistan, whose military leadership does not regard him as a friend and where he will now have direct control over the armed drone campaign that the Pakistani military says it wants stopped.

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 Guantanamo 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.

A former general said the alliance established after 9/11 to get rid of Al Qaeda on Pakistani soil was built on shaky ground, with few aligning interests beyond stopping the terrorist group. Tensions over issues big and small -- like accounting for American grants to the Pakistani military and the failure of the United States to deliver helicopters that would help in counterterrorism efforts -- clouded the hastily arranged alliance from the start, he said.

But now the collision of interests over how to end the war in Afghanistan, and the bitterness over the Davis affair, have exposed deep-seated differences, he said.

The drone campaign, which the C.I.A. has run against militants in Pakistan's tribal areas since 2004, will now become the preserve of General Petraeus, and it has moved to center stage, at least for the Pakistanis. Since Mr. Davis's release from custody in Pakistan after the killings, the C.I.A. has carried out three drone attacks, each one seemingly tied to sensitive events in the United States-Pakistan relationship and aimed at Afghan Taliban militants that Pakistan shelters.

The day after Admiral Mullen left Pakistan last week, a drone attack in North Waziristan killed 23 people associated with Hafiz Gul Barhadur, whose forces are fighting NATO in Afghanistan. Earlier in April, after Lt. Gen. Ahmad Shuja Pasha, the ISI chief, left Washington, a drone attacked another group of Afghan Taliban.

Another former Pakistani general who speaks to General Kayani said he believed that the Pakistan Army's leader had concluded that the drone campaign should end because it hurt the army's reputation among the Pakistani public. Those being killed by the drones are of midlevel or even lesser importance, the general said.

The Americans say the drones are more important than ever as a tool to stanch the flow of Taliban foot soldiers coming across the border to fight American and NATO forces.

The easy access into Afghanistan was on full display last week in Wana, the main town of South Waziristan, according to a local resident.

There, militants loyal to Maulvi Nazir, a Taliban leader who maintains a peace agreement with the Pakistani military and whose forces often cross into Afghanistan, showed high morale and were moving around freely in front of the Pakistani Army, the resident said. "It looked," he said, "as though the army was giving them a free hand."

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