US President Donald Trump knew White House national security adviser Michael Flynn misled his Vice President for weeks before the former general resigned his post on Tuesday.

With the White House in damage control, press secretary Sean Spicer confirmed on Wednesday (AEDT) that President Trump asked for Mr Flynn’s resignation over concerns he misled Vice-President Mike Pence and other officials.

The President had known since late January that Mr Flynn had not given Mr Pence accurate information about his dealings with a top Kremlin officer, Mr Spicer said.

Mr Pence had publicly said Mr Flynn had not been in contact with Russian officials after speaking with the adviser.

The White House was warned by the Justice Department that Mr Flynn was vulnerable to Russian blackmail, according to a Washington Post report published hours before his resignation.

Mr Spicer said the president’s trust in Mr Flynn had “eroded” between that warning and the adviser’s resignation.

"The evolving and and eroding level of trust" led Pres. Trump to ask for Flynn's resignation, Spicer says https://t.co/T5uqoA85rO pic.twitter.com/7jFYSBbOFK

— CBS News (@CBSNews) February 14, 2017

In a resignation letter, Mr Flynn said he held numerous calls with the Russian ambassador to the US during the transition and gave “incomplete information” about those discussions to Mr Pence.

The vice-president, apparently relying on information from Mr Flynn, initially said the national security adviser had not discussed sanctions with the Russian envoy, though Mr Flynn later conceded the issue may have come up.

Mr Trump named retired Lt Gen Keith Kellogg as the acting national security adviser.

However welcomed General Flynn's resignation is, remember that President Trump's Russia connections and intentions are still the real issue. https://t.co/1ngzYtOE8U

— Evan McMullin 🇺🇸 (@EvanMcMullin) February 14, 2017

Mr Kellogg had previously been appointed the National Security Council chief of staff and advised Mr Trump on national security issues during the campaign.

Calls for inquiry

Confirmation Mr Trump had known about Mr Flynn’s misstep for weeks came as Democrats and some Republicans called for an inquiry into the former adviser’s conduct and the White House’s ties with Russia.

Mr Trump has previously said he wanted an improved relationship with Russia and praised Vladimir Putin’s decision not to respond to sanctions imposed by President Obama.

Pressure grew on Mr Flynn to resign after the Washington Post reported the top Trump adviser had been in contact with Russia’s ambassador to the United States on the issue of sanctions.

Leading Republican Senator John McCain said Mr Flynn’s resignation was troubling.

“At the same time, General Flynn’s resignation is a troubling indication of the dysfunction of the current national security apparatus,” the Arizona Republican said.

Michael Flynn (r) had earlier assured Vice-President Mike Pence that he had not discussed sanctions with the Russian envoy.

“General Flynn’s resignation also raises further questions about the Trump administration’s intentions toward Vladimir Putin’s Russia, including statements by the president suggesting moral equivalence between the United States and Russia despite its invasion of Ukraine, annexation of Crimea, threats to our NATO allies, and attempted interference in American elections,” McCain said.

Transcripts of intercepted communications, described by US officials, showed that the issue of US sanctions came up in conversations between Mr Flynn and the ambassador in late December.

The conversations took place around the time that then-president Barack Obama was imposing sanctions on Russia after charging that Moscow had used cyber attacks to try to influence the 2016 presidential election in Mr Trump’s favour.

In his first comment on the resignation, Mr Trump pointed to the many leaks dogging his administration.

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?

— Donald J. Trump (@realDonaldTrump) February 14, 2017

Democrats, who do not have control of Congress, clamoured for more action over Mr Flynn, and asked how much Mr Trump knew about his connections to Russia.

“The American people deserve to know at whose direction General Flynn was acting when he made these calls, and why the White House waited until these reports were public to take action,” Democrat Mark Warner, the Senate intelligence committee’s vice-chairman, said in a statement.

Russian anger

Konstantin Kosachev, chairman of the foreign affairs committee at the upper chamber of the Russian parliament, said in a post on Facebook that firing a national security adviser for his contacts with Russia was “not just paranoia but something even worse”.

He said the resignation suggested Trump had been backed into a corner or that his administration had been “infected” by anti-Russian feeling.

Michael Flynn’s resignation letter posted to Twitter. Source: Twitter.

“Either Trump has not gained the requisite independence and he is consequently being not unsuccessfully backed into a corner, or Russophobia has already infected the new administration also from top to bottom,” Kosachev was cited as saying by the RIA Novosti news agency.

Leonid Slutsky, head of the lower house of parliament’s foreign affairs committee told RIA: “It’s obvious that Flynn was forced to write the letter of resignation under a certain amount of pressure.

“The target was Russia-US relations, undermining confidence in the new US administration. We’ll see how the situation develops further.”