CBS News Correspondent Eric Engberg reports the coffin that Kennedy's body was flown home in was not seen again after the night of November 22, 1963.
JFK's family selected a different one for the burial.
Until Tuesday, when documents denied the public for 33 years became available, the story of how the government dumped the original casket into the Atlantic Ocean was a secret.
It was two years after the assassination and the casket was being stored in a vault at the National Archives in Washington. Concerned it might fall into the hands of sensation seekers, the late president's brother, Robert, told Archives officials: "What I would like to have done is take it to sea."
The actual disposal was turned over to the military and a submarine commander advised on how to make it "secure for dropping and sinking."
Forty-two holes were drilled into the casket, it was weighted down with three 80-pound sandbags and fitted with two parachutes to insure it wouldn't break apart upon impact with the water.
A memo written by an aide to then-Defense Secretary Robert McNamara records how the casket was moved from the Archives to a C-130 transport plane at Andrews Air Force Base on Feb. 18, 1966.
The crew then flew to a point off the Delaware coast and at precisely 10 a.m. the weighted casket was pushed overboard. It sunk "sharply, clearly and immediately...." the memo says.
This latest revelation seems to spawn more questions than answers and will only fuel the numerous JFK conspiracy theories. What's more puzzling is that the new documents don't show anyone seemed worried the top-secret coffin sinking might raise just the sort of questions surrounding the president' assassination that the government was struggling to put down.