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 response 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.
As well as an FBI investigation, both the Senate and House intelligence committees are already examining Russian involvement in the election. It is not yet clear whether the latest claims will be included in their scope.
Why Mr Flynn resigned
He stood down over allegations he discussed US sanctions with a Russian envoy in December, before Mr Trump took office.
The conversations took place about the time that then-President Barack Obama was imposing retaliatory measures on Russia following reports it attempted to sway the US election in Mr Trump’s favour.
Mr Flynn could have broken a law – known as the Logan Act – by conducting 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.
The White House admitted it had been warned about the contacts on 26 January but President Trump initially concluded Mr Flynn had not broken any law.
White House lawyers then conducted a review and questioned Mr Flynn before reaching the same conclusion as Mr Trump, White House spokesman Sean Spicer said, 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.