The warning, which has not been previously reported, came less than 48 hours after the November election when the two sat down for a 90-minute conversation in the Oval Office.
The revelation comes on a day that former acting Attorney General Sally Yates is expected to testify that Flynn misled the White House about his contacts with Russia’s ambassador to the United States.
NBC News has asked the Trump administration for a response.
According to all three former officials, Obama warned Trump against hiring Flynn. The Obama administration fired Flynn in 2014 from his position as head of the Defense Intelligence Agency, largely because of mismanagement and temperament issues.