Mr Foggo's retirement came days after the resignation of Porter Goss
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US federal agents have searched the house and office of the outgoing executive director of the CIA.
Kyle "Dusty" Foggo, formerly the third-ranking official at the spy agency, announced his retirement earlier this week.
He has been linked to a probe into possible corruption involving agency contracts, but denies any wrongdoing.
The raid comes at a time of upheaval for the CIA after the shock resignation of its head, Porter Goss, last week.
FBI agents with warrants searched Mr Foggo's home in Virginia and his office at the CIA headquarters, FBI spokeswoman April Langwell said.
She said Mr Foggo was being investigated by five government agencies.
A CIA spokeswoman, Jennifer Millerwise Dyck, also confirmed the searches and said the agency was "cooperating fully with the Department of Justice and the FBI".
'Properly awarded'
Agencies are reported to have been investigating whether Mr Foggo improperly awarded contracts worth millions of dollars to a personal friend.
Agents searched both Mr Foggo's home and office
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Allegations also link him to a separate scandal involving former Republican congressman Randy Duke Cunningham, already jailed for taking millions of dollars in bribes.
In a statement issued on his behalf by the CIA last week, Mr Foggo denied the allegations.
"Mr Foggo maintains that government contracts for which he was responsible were properly awarded and administered," the statement said. He has not been charged with anything.
Ms Dyck said the investigation into Mr Foggo had "absolutely nothing, zero" to do with the 5 May resignation of Mr Goss.
He has declined to comment on his departure, telling CNN that "it's one of those mysteries". The White House described as "categorically untrue" US media reports that the president had lost confidence in Mr Goss.
But the BBC's James Westhead says the rapidly-moving investigation into Mr Foggo's activities may partly explain the sudden unexpected clear-out of the CIA's top management.