At Trump's behest, press secretary Sean Spicer issued a statement saying that the president was looking into Flynn's private discussions with Moscow's ambassador to Washington and subsequent actions.
Flynn -- the former head of defense intelligence whose encounters with Russian President Vladimir Putin have already drawn criticism -- is accused of discussing the Obama administration's election-hacking-related sanctions with Ambassador Sergey Kislyak.
Flynn had initially claimed he did not discuss sanctions, prompting Vice President Mike Pence to publicly come to his defense.
Flynn now stands accused of inappropriate contacts with a foreign government and of misleading the vice president of the United States. White House officials said that Flynn has since apologized to Pence.
"The president is evaluating the situation," Spicer said, indicating that Trump was speaking to Pence and "various other people about what he considers the single most important subject there is -- our national security."
In the cutthroat world of Washington politics, that could spell the beginning of the end, despite other Trump aides suggesting that Flynn has the full support of the president.
The White House on Monday said that there was nothing wrong with Flynn contacting other governments per se.
"I think general Flynn both during the transition and after, just as part of the job of national security advisor, is to speak with counterparts," said Spicer.
But he was quick to distance the president from any talk of sanctions -- which could be seen as undermining then president Barack Obama's policy and a potential breach of the law.
Asked if the president was aware that Flynn would discuss sanctions with the Russian ambassador, Spicer said: "No, absolutely not. No way."
From inner circle to... ?
Until now, Flynn has been an instrumental player in Trump's inner circle.
He was an early supporter of Trump's improbable bid for the presidency and has encouraged tougher policies on Iran and a softer policy on Russia.
That was a sharp break with the Obama administration, which introduced a wave of sanctions against Moscow over its annexation of Ukraine's Crimea, support for separatists in eastern Ukraine and what US intelligence says were its attempts to sway the 2016 election in Trump's favor.
Washington and Moscow had also clashed over alleged war crimes in Syria, where Russia is accused of aiding the bombing of hospitals and other civilian targets. Despite this, Flynn had argued for rapprochement.
Several Democratic lawmakers have called on Flynn to resign over the situation, which has become a major embarrassment for the ruling Republicans.
He would become the first personnel casualty of Trump's White House, which is less than four weeks old.
'Staggering' allegations
Adam Schiff, the senior Democrat on the House Intelligence Committee, called the allegations "staggering," saying that if they are true, Flynn should resign or be fired.
The issue comes up just days before Trump has his first official talks with Israeli Prime Minister Benjamin Netanyahu, talks in which the president's national security advisor would normally have a key role.
Spicer said that Flynn continues to take part in those preparations.
The Justice Department and Congress are both investigating possible links between Trump campaign advisors and Moscow, and US intelligence has concluded that Putin personally directed an operation to interfere in the US election.
On December 29, the Obama administration sanctioned four Russian individuals and five entities, and expelled 35 Russian diplomats in retaliation.
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