Flynn's departure came soon 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 Sergei Kislyak and was potentially vulnerable to blackmail by the Russians.
58-year-old Flynn, one of the early backers of Trump during his presidential run, remained in the top position of National Security Advisor for just three weeks, making him one of the shortest-serving senior presidential advisers in modern American history.
Flynn, a retired Army lieutenant general, in his resignation letter released by the White House, apologised to President Trump and Vice President Mike Pence for briefing them with incomplete information on his talks with the Russian Ambassador before the swearing in.
"In the course of my duties as the incoming National Security Advisor, I held numerous phone calls with foreign counterparts, ministers, and ambassadors. These calls were to facilitate a smooth transition and begin to build the necessary relationships between the President, his advisors and foreign leaders. Such calls are standard practice in any transition of this magnitude," Flynn wrote in the resignation letter.
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Flynn said he knows with the strong leadership of President Trump and Vice President Pence and the superb team they are assembling, this team will go down in history as one of the greatest presidencies in US history.
"The sudden exit marks the most public display yet of disarray at the highest levels of the new administration, which has faced repeated questions over a slew of controversies and reports of infighting among senior aides during its first three weeks, CNN commented on Flynn's resignation.
He served as the Commander of the 82nd Airborne Division from 1997 to 1998.
Prior to his retirement, General Kellogg was Director of the Command, Control, Communications, and Computers Directorate under the Joint Chiefs of Staff.