A White House official also confirmed the Justice Department warning.
The concern was raised after Flynn claimed he did not discuss with the Russian ambassador the sanctions being imposed by the Obama administration in retaliation for Russia’s interference in the election. Flynn was not yet in government.
The message was delivered by then-Acting Attorney General Sally Yates. Other top intelligence officials, including James Clapper and John Brennan, were in agreement the White House should be alerted about the concerns.
The White House did not immediately respond to a CNN request for comment.