The White House confirmed Flynn's resignation on Monday night. Keith Kellogg, a retired US Army general, has been named as Flynn’s interim replacement.
In his resignation letter, Flynn said he had given incomplete information to Vice President Mike Pence, who went on live TV and denied the allegations against the retired US Army general.
"I inadvertently briefed the Vice President-elect and others with incomplete information regarding my phone calls with the Russian ambassador. I have sincerely apologized to the President and the Vice President, and they have accepted my apology," Flynn wrote.
"I am tendering my resignation, honored to have served our nation and the American people in such a distinguished way," he wrote. "I know with the strong leadership of President Donald J. Trump and Vice President Mike Pence and the superb team they are assembling, this team will go down in history as one of the greatest presidencies in US history."
Flynn's resignation came just hours after reports surfaced that the Justice Department warned President Trump last month that Flynn lied regarding his communications with the Russian ambassador to the US and was potentially vulnerable to blackmail by Moscow.
The conversation, which took place well before Trump’s inauguration, centered around lifting then-President Barack Obama’s sanctions against Russia.
Any discussion of sanctions at that time would have amounted to a breach of law against private citizens engaging in foreign policy.
White House spokesman Sean Spicer said hours before Flynn’s resignation that Trump was "evaluating” the situation and had talked to Pence and "various other people” about the issue.
The news came days after the White House launched an investigation into the matter.
‘Flynn is an open Islamophobe’
US President Donald Trump (right) and his national security adviser, Michael Flynn, arrive at MacDill Air Force Base on February 6, 2017 in Tampa, Florida. (Photo by FP)
Flynn said in August that "Islamism” was a "vicious cancer” in body of all Muslims and had "to be excised.”
"We are facing another 'ism,' just like we faced Nazism, and fascism, and imperialism and communism; this is Islamism, it is a vicious cancer inside the body of 1.7 billion people on this planet and it has to be excised," he said during a speech to the Ahavath Torah Congregation in Stoughton, Massachusetts.
According to Scottish writer and journalist John Wight, "Flynn is an open Islamophobe.”
He told Press TV on Monday that "Flynn seems to carry a particular hatred of Iran. He has talked in the past of the need for 'regime change’ in Iran, and he has described Islam as ‘a malignant cancer.’ That’s a direct quote. He has also described it as a 'sick religion' that requires healing.”
(Press TV)