A second top CIA official is to retire from his post, less than a day after the surprise resignation of the agency's director George Tenet.
Pavitt has been in charge of the CIA's spies for the past five years
James Pavitt, deputy director for operations, is said to have made the decision some weeks ago.
The departures come as the agency is braced for reports expected to criticise its conduct in the run-up to the 9/11 attacks and the war in Iraq.
The CIA says Mr Pavitt's decision was unconnected with Mr Tenet's departure.
But analysts say the move will mean more upheaval at a critical time for the agency.
On Thursday Mr Tenet cited "personal reasons" for his decision to go, but he has faced months of criticism for not preventing the 11 September 2001 attacks, and over the failure to uncover weapons of mass destruction in Iraq.
The BBC's Adam Brookes in Washington says the official 9/11 inquiry is due to report soon and is likely to savage the CIA for failing to stop Osama Bin Laden.
At the same time, another inquiry is investigating what the agency told President George W Bush about weapons of mass destruction in Iraq.
Mr Bush accepted the CIA director's resignation and said he would miss the "strong and able" Mr Tenet as head of the US intelligence agency.
Mr Tenet, 51, will leave the CIA on 11 July when Deputy Director John McLaughlin will take over temporarily.
Department under fire
James Pavitt has worked for the agency for 31 years, five as the deputy director of operations, in charge of the agency's spies.
The CIA has been under pressure for not preventing 11 September
His identity had been unknown until last April when, in an unprecedented move, he appeared publicly before the 11 September commission.
At the time he said the failures that occurred before the attacks were due to woefully inadequate resources, not a lack of caring.
The BBC's Ian Pannell, in Washington, says it is his department's record in gathering intelligence in Iraq that has come in for the strongest criticism.
In particular they are criticised for not having enough good human intelligence on the ground, that they placed too much credence on badly sourced material.
A spokesman for the CIA told the BBC that Mr Pavitt's decision to leave was a retirement not a resignation and that it was emphatically not related to the director's decision to retire.
Still, the timing at the very least appears poor and many of the agency's critics will no doubt interpret this as a sign of crisis at the CIA, our correspondent says.
In a farewell speech to CIA employees, Mr Tenet said his resignation had "only one basis in fact: the well-being of my beautiful family".
Born 5 January 1953 in New York to Greek immigrants
Studied at Georgetown and Columbia universities
Served on Clinton's National Security Council 1992-95
Deputy CIA director 1995-96
Acting CIA director 1996-97
Confirmed as CIA director 1997
Choking back tears, he told his son Michael, a teenager who was sitting in the audience: "You've been a great son - and now I'm going to be a great dad."
Correspondents say Mr Tenet, who has been in the post for seven years, had been widely expected to step down after the November presidential election.
Unusually, Mr Tenet has served under two presidents from different parties, having been appointed by President Bill Clinton.
Following Thursday's surprise announcement, the presumptive Democratic presidential nominee, John Kerry, said he wished Mr Tenet "the very best", but he said the Bush administration had to take responsibility for "significant intelligence failures".
Mr Kerry, who has previously called for Mr Tenet to step down, said this was an opportunity to reform the US intelligence services.
After the 11 September attacks, many commentators thought Mr Tenet's position was at risk - but President Bush stuck by his intelligence chief.
Last July Mr Tenet accepted full responsibility for unsubstantiated allegations about Iraq's weapons programme being included in Mr Bush's State of the Union address.