CIA pulls top spy out of Pakistan as cover is blown

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The CIA has pulled its most senior spy out of Pakistan when his cover was blown after being named in a lawsuit that accused him of killing civilians in missile strikes.

The Islamabad station chief was hastily withdrawn on safety grounds after a series of death threats were made against him. The name of the reputed agent appeared on a series of placards during anti-American protests against the drone strikes and appeared in Pakistan media.

The spy's removal came as three American missile strikes killed 54 alleged militants inside Pakistan, close to the Afghan border. Pakistani officials claimed that the dead included commanders of a Taliban-allied group who were holding a meeting.

The attacks took place in the Khyber tribal region, which has been rarely struck by American missiles over the last three years. The strikes could indicate a possible expansion of the CIA-led covert campaign of drone strikes inside Pakistani territory.

The Obama administration has intensified missile attacks in northwest Pakistan since taking office and they often happen several times a week.

The US is desperate to weaken insurgent networks that US officials say are behind much of the violence against US troops just across the frontier in Afghanistan. There have been more than 100 drone strikes this year, more than double the number from 2009.

The Islamabad station chief, one of the CIA's most sensitive positions, runs the drone programme and works closely with the Pakistan's intelligence service, the ISI. The lawyer bringing the case – which also named the CIA's director, Leon Panetta, and the Defence Secretary, Robert Gates – said he got the agent's name from local journalists. A Pakistani intelligence officer told the Associated Press agency that the ISI had no clue how the name had leaked. However, there were reports last night that the agent had been wrongly identified by the Pakistani lawsuit.

"Our station chiefs routinely encounter major risk as they work to keep America safe, and they've been targeted by terrorists in the past," the CIA spokesman George Little said. "They are courageous in the face of danger, and their security is obviously a top priority for the CIA, especially when there's an imminent threat."

Agents have previously been withdrawn when their cover was blown, including in 1999, when an Israeli newspaper revealed the identity of the station chief in Tel Aviv. Another station chief was named in 2001 in Argentina.

The threats that were made against the station chief in Pakistan in the wake of his name being revealed were "of such a serious nature that it would be imprudent not to act," one senior US official said on condition of anonymity.

Washington is especially keen to the perils that its operatives face in Pakistan, not least because memories that still linger of the kidnapping and subsequent killing there by al-Qa'ida of the Wall Street Journal Asia bureau chief there, Daniel Pearl, in 2002.

Human rights groups have repeatedly criticised the use of drone attacks, saying that they have led to many innocent civilian deaths.