CIA chief in Pakistan pulls out after clashes

The CIA station chief who oversaw the intelligence work before the raid that killed Osama bin Laden has been pulled out of Islamabad – the second time in seven months that the CIA's top spy in Pakistan has been replaced.

The station chief was evacuated for "medical reasons" a fortnight ago. But an official familiar with CIA-ISI relations told The Independent that the US's top clandestine officer was due to be replaced in September, after just 10 months on the job. The illness, the official added, merely "expedited" his recall. The station chief will not be returning to Pakistan.

While the change of station chiefs so soon is highly unusual, it may alleviate strained relations between Washington and Islamabad. The station chief had clashed with his own ambassador, Cameron Munter, over the use of drones during diplomatic negotiations.

The station chief's relationship was even worse with the head of Pakistan's Inter-Services Intelligence (ISI) agency. Since the Raymond Davis affair, when a CIA contractor killed two men linked to the ISI in January, the pair have repeatedly clashed. The exchanges grew more intemperate after the Bin Laden raid. Evidence of the hostilities came just weeks after the al-Qa'ida leader's death, when the station chief's name was leaked to the local press. The name was slightly misspelled, but compromised the CIA agent's cover. The previous station chief was forced to leave in December after his identity was exposed.

The change of station chiefs comes against the backdrop of enduring tensions between the two spy agencies. US and Pakistani officials told The Independent that the poor intelligence relationship is bleeding over into other areas of co-operation.

General Pasha met the acting CIA director, Mike Morrell, in Washington on 14 July to decide on new "rules of engagement". "It is now our policy that everything now be set down in writing," said a senior Pakistani military official. Pakistan has granted 87 visas to CIA agents, a concession that comes after months of choking the number of Americans travelling to Pakistan.

But other key disputes remain. Since the Davis affair, General Pasha has been determined to shut down all unauthorised or "non-official cover" CIA activities inside Pakistan. His alarm was heightened when it emerged that the CIA used Pakistanis to help spy on the al-Qa'ida leader's hiding place in Abbottabad, a garrison town.

A US official said that the ISI chief was trying determine, through various means, what each American was working on, in an attempt to shut down any clandestine activities outside the Pakistani spy agency's knowledge.

US officials complain that they have been "harassed" inside Pakistan for months now. Their movements were recently restricted. But after negotiations, Pakistan has issued permission for American diplomats to travel freely for a month. Another dispute is over the use of drones. Pakistan wants the CIA to either stop the drones, or only resume them with its co-operation.