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The source said the CIA had briefed other parts of the US government on its assessment, which contradicts Saudi government assertions that Prince Mohammed was not involved.
The CIA's finding, first reported by the Washington Post, is the most definitive US assessment to date tying Saudi Arabia's de facto ruler directly to the killing.
Both the White House and the State Department declined to comment.
Khashoggi, a critic of the Saudi government and a columnist for the Washington Post, was killed at the Saudi consulate in Istanbul on Oct. 2 when he went there to pick up documents he needed for his planned marriage to a Turkish woman.
Khashoggi had resisted pressure from Riyadh for him to return home. Saudi officials have said a team of 15 Saudi nationals were sent to confront Khashoggi at the consulate and that he was accidentally killed in a chokehold by men who were trying to force him to return to the kingdom.
Turkish officials have said the killing was intentional and have been pressuring Saudi Arabia to extradite those responsible to stand trial. An adviser to Turkish President Tayyip Erdogan on Thursday accused Saudi Arabia of trying to cover up the murder.