WASHINGTON  The Central Intelligence Agency’s top clandestine officer in Pakistan’s capital, Islamabad, was removed from the country on Thursday amid an escalating war of recriminations between American and Pakistani spies, with some American officials convinced that the officer’s cover was deliberately blown by Pakistan’s military intelligence agency.

The American spy’s hurried departure is the latest evidence of mounting tensions between two uneasy allies, with the Obama administration’s strategy for ending the war in Afghanistan hinging on the cooperation of Pakistan in the hunt for militants in the mountains that border those two countries. The tensions could intensify in the coming months with the prospect of more American pressure on Pakistan.

As the cloak-and-dagger drama was playing out in Islamabad, 100 miles to the west the C.I.A. was expanding its covert war using armed drones against militants. Since Thursday, C.I.A. missile strikes have killed dozens of suspects in Khyber Agency, a part of the tribal areas in Pakistan that the spy agency had largely spared until now because of its proximity to the sprawling market city of Peshawar.

American officials said the C.I.A. station chief had received a number of death threats since being publicly identified in a legal complaint sent to the Pakistani police this week by the family of victims of earlier drone campaigns.