The files comprise almost the final one per cent of records held by the federal government and their publication follows a release in July when the record-keepers, the National Archives, posted nearly 3,000 documents online, mostly formerly released documents with previously redacted portions.
The documents revealed the CIA's role in foreign assassinations said plans to assassinate Castro were undertaken in the early days of the Kennedy administration, CNN reported.
The documents also revealed that the FBI had got a death threat on assassin Lee Harvey Oswald the day before his murder it said.
The files also revealed a national security council document from 1962 -- before Kennedy's murder -- referenced 'Operation Mongoose', a covert attempt to topple communism in Cuba.
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In the minutes of a secret meeting on Operation Mongoose from September 14,1962, "General (Marshall) Carter said that the CIA would examine the possibilities of sabotaging airplane parts which are scheduled to be shipped from Canada to Cuba", the report said.
The newly released documents also reveal that Soviet Union leaders considered Oswald a "neurotic maniac who was disloyal to his own country and everything else", according to an FBI memo documenting reactions in Russia to the assassination.
The files also showed that the Soviet officials feared a conspiracy was behind the death of Kennedy, perhaps organised by a rightwing coup or Kennedy's successor Lyndon Johnson.
However, at the request of security agencies, Trump agreed to withhold some files. He ordered that they be reviewed in the next 180 days.
"This temporary withholding from full public disclosure is necessary to protect against harm to the military defence, intelligence operations, law enforcement, or the conduct of foreign relations that is of such gravity that it outweighs thepublic interest in immediate disclosure," Trump said in a statement.
"The President has demanded unprecedented transparency from the agencies and directed them to minimise redactions without delay," White House Press Secretary Sarah Sanders said.
The National Archives will therefore release more records, with redactions only in the rarest of circumstances, by the deadline of April 26, 2018, she said.
Early this year on July 24, the National Archives had released 3,810 related records, including 441 records previously withheld in their entirety and 3,369 records previously withheld in part.
According to the National Archives, the final batch includes information on the Central Intelligence Agency's station in Mexico City, where Oswald showed up weeks before Kennedy's death.
There are also documents mentioning James Jesus Angleton, the agency's counterintelligence chief, at the time who took over the CIA's post-assassination investigation.