The President had Tweeted that he would release the files to the world after decades in the dark but has now decided to follow the recommendations of his security agencies.
Some 2,800 of the 3,200 records have been published by The National Archive as the remaining papers stay under lock and key.
Lobbying from agents within the security forces forced the climb down.
Members of the administration have declined to comment on what is contained within the files and whether they are related to any popular conspiracy theories surrounding the death of President John F Kennedy.
The President issued a memo reading: “The American public expects and deserves its government to produce as much access as possible to the John F Kennedy assassination records.
“I am ordering today that the veil finally be lifted.”
President Trump claimed he has “no choice” but to keep parts of the investigation secret following advice from law enforcement, in a move bound to set conspiracy theories running.
Trump ordered a 180—day review forcing government agencies to justify why the documents could not be seen by the American public.
He reportedly expects it to be rare for the review to find any remaing files that cannot be released.
Officials who requested anonymity told reporters the President was reluctant to hold back thousands of pages of the secret files but felt the agencies had given him no choice.
One unnamed official said: “The President wants to ensure there is full transparency here and is expecting that the agencies do a better job in reducing any conflicts within the redactions and get this information out as quickly as possible.”
Kennedy expert, Larry Sabato, claims the CIA blocked the release of the papers to keep names and other information secret.