In November 1963, President Lyndon B. Johnson appointed Ford to the Warren Commission, a special task force set up to investigate the assassination of President John F. Kennedy. Ford was assigned to prepare a biography of Lee Harvey Oswald, the accused assassin. The Commission's work continues to be debated in the public arena.
In the foreword to his book, A Presidential Legacy and The Warren Commission, Ford said the CIA destroyed or kept from investigators critical secrets connected to the 1963 assassination of President John F. Kennedy. He said the commission's probe put "certain classified and potentially damaging operations in danger of being exposed.
According to a 1963 FBI memo released in 2008, Ford secretly provided the FBI with information regarding two of his fellow commission members, both of whom were dubious about the FBI's conclusions regarding the assassination. The FBI position was that President Kennedy was shot by a single gunman firing from the Texas Book Depository. Another 1963 memo released in 1978 stated that Representative Ford volunteered to advise the FBI regarding the content of the commission's deliberations, provided that his involvement with the bureau was kept confidential, a condition which the bureau approved. Ford generally believed in the single assassin theory. According to the same reports, Ford generally had strong ties to the FBI and J. Edgar Hoover.