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.” ….

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