The explosive new development on Tuesday followed a week of tumult at the White House after Trump fired Comey and then discussed sensitive national security information about Islamic State with Russian Foreign Minister Sergei Lavrov.
The Comey memo, first reported by the New York Times, caused alarm on Capitol Hill and raised questions about whether Trump tried to interfere with a federal investigation.
The White House quickly denied the report, saying in a statement it was "not a truthful or accurate portrayal of the conversation between the president and Mr. Comey."
Comey wrote the memo after he met in the Oval Office with Trump, the day after the Republican president fired Flynn on February 14 for misleading Vice President Mike Pence about the extent of his conversations last year with Russia's ambassador, Sergei Kislyak.
"I hope you can let this go," Trump told Comey, according to a source familiar with the contents of the memo.
The New York Times said that during the Oval Office meeting, Trump condemned a series of government leaks to the news media and said the FBI director should consider prosecuting reporters for publishing classified information.
Coming the day after charges that Trump disclosed sensitive information to the Russians last week, the new disclosure further rattled members of Congress.
"The memo is powerful evidence of obstruction of justice and certainly merits immediate and prompt investigation by an independent special prosecutor," said Democratic US Senator Richard Blumenthal.