The move comes one day after CNN filed a lawsuit asking the agency to release the documents.
Comey described the meetings and his note-taking in detail last week while testifying before the Senate intelligence committee.
Despite high public interest in the content of the memos, Comey's testimony that the records are not classified and a ruling from the Justice Department that the FBI should expedite CNN's FOIA request for the memos, the FBI has not provided either the documents or a reason to withhold them, according to the lawsuit filed in the US District Court for the District of Columbia.
That constitutes a violation of the federal Freedom of Information Act, the lawsuit alleges. CNN asked the court to require the agency release the documents "unredacted, and without further delay."
Friday, the FBI formally denied the FOIA request for the Comey memos, citing a law enforcement exemption.
What the memos say
Before he was fired, Comey was overseeing the investigation into whether members of Trump's campaign team participated in Russian interference with the 2016 presidential election.
In riveting testimony last week, Comey detailed how prior to the firing, Trump invited and corralled him into a series of private meetings. He said the conversations were uncomfortable enough that he documented them in a series of nine memos initially distributed to only a small circle of FBI colleagues.
The memos, he said, are evidence that Trump urged him to end one strand of the investigation involving Trump's former national security adviser Michael Flynn, pledge loyalty to the President and state publicly that the FBI was not investigating Trump himself.
Comey rejected those requests and the investigation continued. Trump has denied several of Comey's claims, and his lawyer criticized what he called attempts to "undermine this administration with selective and illegal leaks of classified information and privileged communications."
After details of one memo were made public by The New York Times, Comey told Congress that he was responsible for the disclosure. He said he provided one of the documents to a friend and requested the details be shared with the media.
Comey testified that he hoped the news would "prompt the appointment of a special counsel," which indeed happened several days later.
He said his copies are now in the possession of the special prosecutor, Robert Mueller, and his friend said he returned his copy to the FBI.