The officer "is returning to the United States after the decision was taken that terrorist threats against him in Pakistan were of such a serious nature that it would be imprudent not to act," a US intelligence official said.
"The CIA's mission in Pakistan, including the agency's relentless fight against militants, continues unabated," said the official.
Current and former US national security officials said there was strong suspicion in Washington that the name of the CIA official had been deliberately leaked by elements of Pakistan's Inter-Services Intelligence agency (ISI).
A lawsuit filed earlier this month in Pakistan, accused one Jonathan Banks of being responsible for killing civilians in missile strikes as part of the CIA's covert programme.
Yesterday, three American missile attacks killed 54 alleged militants close to the Afghan border, an unusually high number of victims that included commanders of a Taleban-allied group that were holding a meeting, Pakistani officials said.
The attacks took place in the Khyber tribal region, which has been rarely struck by American missiles before over the last three years, and could indicate a possible expansion of the CIA-led campaign of drone strikes inside Pakistani territory.
"It is highly unlikely that the chief of station would have been identified by name without at least tacit approval from ISI," said a senior congressional aide.
"This should be interpreted as a message from the Pakistani intelligence service that they are still in control of intelligence-gathering in their country."
As Pakistan's principal intelligence and counter-terrorism agency, ISI is regarded by American officials as a critical player in operations against al-Qaeda and other militant groups using Pakistan as a sanctuary and staging area for attacks in neighbouring Afghanistan and elsewhere.
However, American officials have long believed that elements of ISI are sympathetic to, or even collaborating with, militants.
US officials say they have detected a significant deterioration in relations between the Pakistani spy agency and its Americancontacts.
Some American officials said they believe ISI elements may have leaked the identity of the CIA officer in retaliation for the filing of a private civil lawsuit in a New York federal court against ISI and Lashkar-e-Taiba, a Pakistan based militant group, by the family of a Jewish couple who were killed during a 2008 attack on hotels and other targets in Mumbai by militants linked to Lashkar-e-Taiba.
Experts on the relationship between ISI and Pakistani militant groups believe some ISI elements are close to Lashkar-e-Taiba and may have helped create the militant group.
The station chief had served in Pakistan for several years. He had remained on assignment there beyond the normal tour of duty for a station chief, intelligence sources said.