Robert F Kennedy Jr said his father (Robert Kennedy) believed that the Warren Commission report, which concluded Lee Harvey Oswald acted alone in killing the president, was a "shoddy piece of craftsmanship."
The mystery of the November 22, 1963 assassination were retouched by Kennedy and his sister Rory at a Friday night interview aired in the same city where the killing took place and come as a year of observances begins for the 50th anniversary of the president's death.
Dallas Morning Herald quoted Robert F Kennedy Jr and his sister for the remarks while appearing on a PBS talk show hosted by Charlie Rose.
JFK's brother, former US Attorney General Robert Kennedy had publicly supported the Warren Commission, but privately had serious reservations, his son said.
Robert said his father at the time of his uncle's death had serious doubts about the accuracy of the Warren Report and his US Justice Department investigators looked into the allegations the assassin had received aid from the Mafia, the CIA or other organisations.
Robert, who was nine at the time of presidents death did not clarify if his father was convinced that such groups were involved. "My father thought that somebody was involved."
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He also recollected about president's widow, Jacqueline Kennedy who spent much of the five years after the assassination outside the country because she feared for her children's safety.
Robert F Kennedy Jr, 58, an environmentalist is the third child of Senator Robert F Kennedy, and Rory Kennedy, 44, is an Emmy Award-winning documentary filmmaker and the 11th child.
Their father was assassinated in a Los Angeles hotel, five years later, while celebrating his win in the California Democratic presidential primary.