The White House issued a furious denial after the notes were disclosed late on Tuesday, near the end of a tumultuous day spent beating back potentially disastrous news reports from dawn to dusk.
The bombshell Comey news came as the beleaguered administration was still struggling to explain Monday's revelation that the president had disclosed highly classified information to the Russian foreign minister and the country's ambassador to the United States.
Defending Trump's actions, officials played down the importance and secrecy of the information, which had been supplied by Israel under an intelligence-sharing agreement.
Trump himself said he had "an absolute right" as president to share "facts pertaining to terrorism" and airline safety with Russia.
As for Comey, whom Trump fired last week, the FBI director wrote in a memo after a February meeting at the White House that the new president had asked him to shut down the FBI's investigation of Flynn and his Russian contacts, said a person who had read the memo.
The Flynn investigation was part of a broader probe into Russian interference in last year's presidential election.
Jason Chaffetz, Republican chairman of the House oversight committee, sent a letter to the FBI on Tuesday requesting that it turn over all documents and recordings that detail communications between Comey and Trump.
John McCain, chairman of the Senate Armed Services Committee, said the developments had reached "Watergate size and scale."
The person who described the Comey memo to the AP was not authorized to discuss it by name and spoke on condition of anonymity.
The existence of the memo was first reported on Tuesday by The New York Times.
The White House vigorously denied it all. "While the president has repeatedly expressed his view that General Flynn is a decent man who served and protected our country, the president has never asked Mr. Comey or anyone else to end any investigation, including any investigation involving General Flynn," a White House statement said.
Mark Warner of Virginia, top Democrat on the Senate intelligence committee, said he would ask Comey for additional material as part of that panel's investigation. "Memos, transcripts, tapes - the list keeps getting longer," he said.
The highly classified information about an Islamic State plot was collected by Israel, a crucial source of intelligence and close partner in the fight against some of the America's fiercest threats in the Middle East.