The bureau stated on Monday that the remaining documents would be released by The National Archives on a rolling basis in the coming weeks.
The withheld papers will contain redactions to protect the individuals still alive who provided information during the investigation of the John F Kennedy’s death.
But as time progresses, the FBI said they will attempt to remove the redactions where possible.
News of the impending release of remaining files comes after Donald Trump declared he will release all documents related to President Kennedy’s assassination, despite pleas from US national security agencies to keep some files secret.
The decision to release all remaining documents came after President Trump consulted with Chief of Staff, John Kelly, and national security agencies.
Trump declared all files “other than the names and addresses of any mentioned person who is still living” will be released.
He tweeted: “I am doing this for reasons of full disclosure, transparency and in order to put any and all conspiracy theories to rest.”
The announcement came after Trump put a last minute stop to the release of hundreds of files on the Kennedy assassination, saying he had “no choice” because of “potentially irreversible harm” to national security, law enforcement and foreign relations.
The President stated his intention to have more documents released, but two officials said there was not enough time to go through hundreds of files the agencies wanted to keep secret.
More than 2,800 records have already been made public as the administration started to release documents last week.
One White House officials said “Trump was unhappy with the level of redactions” and went on to add that he believed the agencies were “not meeting the spirit of the law.”
Press secretary, Sarah Sanders recently declared that Trump “has demanded unprecedented transparency from the agencies and directed them to minimise redactions without delay”.
The President promised to release more of the secret files but previously did not commit to making them public.
He tweeted: “JFK Files are being carefully released. In the end there will be great transparency. It is my hope to get just about everything to public!”
Trump’s decision to begin releasing the documents came at the end of a month-long review of the classified files.