The embattled former general had resigned after eroding the US president's trust in him, said the White House press secretary. The remarks appear to contradict Trump's earlier comment: "I don't know about that."
US President Donald Trump knew former national security adviser Michael Flynn misled US officials, including Vice President Mike Pence, for "weeks," White House spokesman Sean Spicer said on Tuesday.
"We've been reviewing and evaluating this issue with respect to General Flynn on a daily basis for a few weeks, trying to ascertain the truth," Spicer said.
However, Trump did not ask for his resignation until Monday. The president's trust in Flynn "had eroded to a point where he felt he needed to make a change," Spicer told reporters.
Trump on Friday said he was not familiar with a report by American daily "Washington Post" that revealed the former national security adviser had failed to clearly elucidate his calls with Russia's ambassador to the US concerning sanctions.
"I don't know about that. I haven't seen it. What report is that? I haven't seen that. I'll look into that," the US president told reporters on Friday.
The revelations have put the White House on the defensive concerning Moscow despite the Trump administration's desire to reset US-Russia relations, which hit a post-Cold War low during former President Barack Obama's tenure.
In his resignation letter, Flynn apologized for failing to provide the vice president and other White House officials on the details of his calls with the Russian diplomat.
"Unfortunately, because of the fast pace of events, I inadvertently briefed the vice president-elect and others with incomplete information regards my phone calls with the Russian ambassador," Flynn wrote.
"I have sincerely apologized to the president and the vice president, and they have accepted my apology," he added.
Before the inauguration, questions had been raised concerning the retired general's ties with Moscow after images emerged online showing him sitting next to Russian President Vladimir Putin at a banquet hosted by state broadcaster RT (formerly Russia Today).
Probe 'highly likely'
Leading Republican Senator Mitch McConnell said the Senate's intelligence committee is likely to review contacts between Flynn and the Russian ambassador.
"The intelligence committee is already looking at Russian involvement in our election … it's highly likely they'd want to take a look at this episode, they have the jurisdiction to do it," McConnell said on Tuesday after the White House press.
Before Flynn's resignation, Kremlin spokesman Dmitry Peskov on Monday told reporters that Russian diplomats had not discussed US sanctions against Moscow. However, Peskov on Tuesday described the resignation as "internal business."