Leading members of the US Republican Party have joined calls for a wide investigation into the former national security adviser’s links with Russia.
Michael Flynn quit on Monday over claims he discussed US sanctions with Russia before Donald Trump took office.
On Tuesday, a White House spokesman said Mr Trump knew weeks ago there were problems with the Russia phone calls.
But calls for an independent investigation have encountered a cold reaction from some senior Republicans.
The development came as the New York Times reported that phone records and intercepted calls show members of Mr Trump’s presidential campaign, as well as other Trump associates, “had repeated contacts with senior Russian intelligence officials in the year before the election”.
However, officials spoken to by the newspaper said they had not yet seen evidence that the Trump campaign colluded with Russia on the hacking of the Democratic National Committee or to influence the election.
Why Mr Flynn resigned
He stood down over allegations he discussed US sanctions with a Russian envoy before Mr Trump took office.
It would have been illegal for Mr Flynn to conduct US diplomacy as a private citizen, before he was appointed as national security adviser.
The retired army lieutenant-general initially denied having discussed sanctions with Ambassador Sergei Kislyak. Vice-President Mike Pence publicly denied the allegations on his behalf.
Acting Attorney General Sally Yates had warned the White House about the contacts and that Mr Flynn might be vulnerable to Russian blackmail on 26 January, said White House spokesman Sean Spicer.
Mr Trump had initially concluded that Mr Flynn’s actions did not violate any law, according to Mr Spicer.
The White House counsel then conducted an extensive review and questioned Mr Flynn on multiple occasions before arriving at the same conclusion as Mr Trump, Mr Spicer added. But the trust had gone.
“In the end, it was misleading the vice-president that made the situation unsustainable,” White House Counsellor Kellyanne Conway said on Tuesday.
Mr Flynn was also reportedly questioned by FBI agents in his first days as national security adviser, according to US media.
What Mr Flynn says
In an interview conducted with the conservative website The Daily Caller on Monday, but published only on Tuesday, Mr Flynn said he “crossed no lines” in his conversation with the ambassador.
He said he discussed the expulsion of 35 Russian diplomats over alleged hacking ahead of the election, but “it wasn’t about sanctions”.
He said he was concerned that the apparently classified information had been leaked. “In some of these cases, you’re talking about stuff that’s taken off of a classified system and given to a reporter,” he said. “That’s a crime.”
However, in his resignation letter, Mr Flynn said “the fast pace of events” during the presidential transition meant that he had “inadvertently briefed the vice-president elect and others with incomplete information regarding my phone calls with the Russian ambassador”.