Flynn was asked to quit Monday after it became public that he had misled Vice President Mike Pence about whether he had discussed US sanctions during pre-inauguration phone calls with the Kremlin's man in Washington, Sergey Kislyak.
In new developments Tuesday, it emerged that President Donald Trump was told on January 26 -- more than two weeks ago -- that the Justice Department had concerns about Flynn's conduct.
Pence did not find out he had been misled until February 9, according to two administration officials.
"It's not that he was being left out. It was a legal review," one source said.
When Pence began his inquiry based on Washington Post reporting
, "the timeline moved fast," the source said.
A subsequent review by White House counsel Donald McGahn found that he had not broken the law in his conversations with the Russian envoy. If Flynn discussed detailed policy with the Russian envoy, he could have theoretically infringed the Logan Act that prevents private citizens negotiating with foreign governments over their disputes with the United States.
Trump spokesman Sean Spicer said Flynn's resignation was precipitated not by misconduct but by a gradual erosion of the President's confidence in him, including over a "series of other questionable instances."
"The level of trust between the President and Gen. Flynn had eroded to the point where he felt he had to make a change," Spicer told reporters Tuesday during his daily briefing. "The President was very concerned that Gen. Flynn had misled the vice president and others."
A senior administration official later told CNN the other "questionable instances" included Flynn's request for a security clearance for his son during the transition. He requested the clearance without telling Pence, who at the time was in charge of the transition.
Trump's growing skepticism about Flynn, however, did not prevent the national security adviser from spending the weekend before his ouster with Trump at his Mar-a-Lago resort during a meeting with Japanese Prime Minister Shinzo Abe.
Spicer's attempts to put out the firestorm are unlikely to end the saga, not least because several prominent Republicans on Tuesday joined Democrats in calling for congressional probes into Trump's ties to Moscow, an explosive issue given allegations by the US intelligence community that the Kremlin intervened in the presidential election to help him.
Tuesday's developments also left key questions in the intrigue unanswered -- including why it took Trump more than two weeks to push Flynn out after he learned that his national security adviser had not told the truth to Pence.
Flynn was eventually asked to resign on a dramatic day of confusion and conflicting messages from the West Wing, hours after the publication of a Washington Post report that revealed the Justice Department's warning to the White House counsel's office.
Adding to the drama, a White House official said on Tuesday afternoon that the FBI, which is already investigating alleged contacts between Trump surrogates and Russian officials and intermediaries, interviewed Flynn in the early days of the administration about the calls to the Russian ambassador.
The cloud of suspicion still lingering over the White House due to the Flynn affair comes as the new administration is embroiled in multiple controversies and internal staff are infighting as it struggles to find its feet.
It also thrusts Trump's relationship and admiration for Russian President Vladimir Putin back in the spotlight.
Many Washington power players have been astonished by the President's frequent defenses of the Russian leader and determination to improve relations with the Kremlin, despite Moscow's turn to Cold War-style confrontational policies in recent years.
Those questions are prompting Republican senators to get more aggressive in searching for answers, despite some resistance to a wider probe in the House.
Senate Republican Majority Leader Mitch McConnell said it was "highly likely" that the chamber's intelligence committee would look at allegations that Flynn spoke about sanctions with Kislyak.
Sens. John Cornyn, the No. 2 Republican, Roy Blunt and Lindsey Graham also called for an investigation.
"I think Congress needs to be informed of what actually Gen. Flynn said to the Russian ambassador about lifting sanctions," Graham told CNN's Kate Bolduan on "At This Hour."
"And I want to know, 'Did General Flynn do this by himself or was he directed by somebody to do it?' " the South Carolina Republican added.
Democrats on Capitol Hill already smell blood, and are demanding congressional probes.
"Let's be clear -- right now, there are way more questions than answers on President Trump's relationship with Russia," Sen. Chris Murphy, D-Connecticut, told reporters.
Virginia Sen. Mark Warner, the top Democrat on the Senate intelligence committee said, "The American people deserve to know at whose direction Gen. Flynn was acting when he made these calls, and why the White House waited until these reports were public to take action."
But the President and some House Republicans pushed back, trying to focus attention on the source of disclosures about Flynn's contacts with Russia that appear to have emerged from intelligence surveillance of the Russian Embassy.
"The real story here is why are there so many illegal leaks coming out of Washington? Will these leaks be happening as I deal on N.Korea etc?" Trump tweeted in his first public reaction to Flynn's departure.
House intelligence committee Chairman Devin Nunes said the focus of any investigation should be how news of Flynn's calls leaked out.
Democrats and some Republicans are also asking whether Trump instructed Flynn to talk to the Russian ambassador last year about sanctions imposed by the Obama administration to punish alleged Russian interference in the presidential election.
Russia did not respond in its normally aggressive way to the expulsion of alleged agents from its diplomatic posts in the US and the closure of several compounds allegedly used for espionage activities, leading to suspicion that it believed that the Trump administration would act in a way more conducive to Moscow's position.
But Spicer insisted Trump had given no instructions to Flynn to talk about sanctions with Russia.
"Absolutely not, no, no, no," Spicer said.
Correction: In an earlier version of the story, a reference to Senate Majority Leader Mitch McConnell's comments should have made clear he was talking about allegations surrounding Michael Flynn.