Mr Flynn's departure less than one month into the Trump administration marks an extraordinarily early shakeup in the US President's senior team of advisers.
In his resignation letter, Mr Flynn said he held numerous calls with the Russian ambassador during the transition and gave "incomplete information" about those discussions to Vice-President Mike Pence.
"In the course of my duties as the incoming national security adviser, I held numerous phone calls with foreign counterparts, ministers and ambassadors," Mr Flynn said in his resignation letter.
"These calls were to facilitate a smooth transition and begin to build the necessary relationships between the President, his advisers and foreign leaders.
"Such calls are standard practice in any transition of this magnitude.
"Unfortunately, because of the fast pace of events, I inadvertently briefed the Vice-President elect and others with incomplete information regarding my phone calls with the Russian ambassador. I have sincerely apologised to the President and the Vice-President, and they have accepted my apology."Mr Pence, 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.
Donald Trump has named retired Lieutenant General Keith Kellogg as the acting national security adviser.
Source - ABC/AP