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The director of the CIA was part of the cover-up of the assassination of President John F Kennedy , it has sensationally been claimed.

Fifty years after JFK's death, the spy agency appears to acknowledge that there was impropriety within its ranks in a once-secret report.

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CIA chief John McCone was allegedly at the heart of a "benign cover-up" over Kennedy's assassination in November 1963, POLITICO Magazine reports .

The spymaster and other senior CIA officials are accused of withholding "incendiary" information from the Warren Commission, set up by President Lyndon Johnson to investigate JFK's murder.

(Image: Getty)

According to the report by top CIA historian David Robarge, the cover-up was intended to keep the commission focused on “what the Agency believed at the time was the ‘best truth’—that Lee Harvey Oswald, for as yet undetermined motives, had acted alone in killing John Kennedy.”

McCone, who died in 1991, is accused of withholding important information about the existence of CIA plots to assassinate then-Prime Minister of Cuba, Fidel Castro, POLITICO reports.

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McCone is said to have been quickly convinced that Oswald acted as a lone wolf with no accomplices in Cuba or elsewhere and so directed the CIA to provide only “passive, reactive and selective” assistance.

Thus the Warren Commission never knew to ask questions or further investigate any potential ties to Cuba or anyone who wanted Kennedy dead in retaliation for the Castro plots.

The report, which was declassified in 2013, also suggests McCone withheld evidence that the CIA may have been in communication with Oswald before 1963.

It is also suggested that the spy agency secretly monitored Oswald’s mail after he attempted to defect to the Soviet Union in 1959, according to POLITICO.

(Image: Getty)

Robarge draws no conclusions on McCone's motivation but suggests that the White House administration under Johnson may have directed him to hide information.

The report was originally published in the CIA's internal magazine, Studies in Intelligence, and is now available on The George Washington University’s National Security Archive website .