The CIA station chief was in transit Thursday after a Pakistani lawsuit earlier this month accused him by name of killing civilians in missile strikes. The Associated Press is not publishing the station chief's name because he remains undercover and his name is classified.
CIA airstrikes from unmanned aircraft have successfully killed terrorist leaders but have led to accusations in Pakistan that the strikes have killed innocent people. The U.S. does not acknowledge the missile strikes, but there have been more than 100 such attacks this year - more than double the amount in 2009.
The lawsuit blew the American spy's cover, leading to threats against him and forcing the U.S. to call him home, the officials said, speaking on condition of anonymity because of the sensitivity of the issue.
CIA officials' "serious concerns" for the station chief's safety led to the decision to bring him home, a U.S. official said. A spokeswoman for the spy agency, Jennifer Youngblood, declined to comment.
The Pakistani lawsuit also named CIA Director Leon Panetta and Defense Secretary Robert Gates.