Censor.NET reports referring to CNN.
"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, according to a copy of his resignation letter obtained by CNN.
His departure came just after reports surfaced the Justice Department warned the Trump administration last month that Flynn misled administration officials regarding his communications with the Russian ambassador to the United States and was potentially vulnerable to blackmail by the Russians.
Flynn also wrote he knew that "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 U.S. history."
The move comes less than a month into the job, making him one of the shortest-serving senior presidential advisers in modern history.
An administration source said that Trump "hung in there" when it came to Flynn, but there was a "flood of information" that finally made it clear he had to resign.
Earlier, media reported that a few weeks prior to Donald Trump's inauguration as U.S. president, his National Security Advisor Michael Flynn had discussed U.S. sanctions against Russia and areas of possible cooperation with the ambassador of this country in the United States.
In January, the U.S. counterintelligence investigation probed Flynn's phone calls, including those with the Russian ambassador in late December.
Flynn, in turn, assured colleagues in the White House that he hadn't discussed sanctions with Russian Ambassador Kislyak. Vice-President Mike Pence, White House Chief of Staff Raines Pribus and White House Spokesman Sean Spicer believed him and publicly declared his noninvolvement.