Flynn did not concede any wrongdoing in his resignation letter, saying that he inadvertently briefed Vice President Mike Pence and others with incomplete information regarding his phone calls with the Russian ambassador.
"General Flynn's security clearance has been suspended pending review," the DIA spokesperson was quoted as saying by CNN on Wednesday.
The former National Security Adviser served as director of the DIA from 2012 to 2014, but was fired by former President Barack Obama for allegedly mismanaging the agency.
Flynn will likely be subjected to a 13-point adjudication process to determine, among other things, how the telephone conversations with Russian officials affected is allegiance to the United States and if he was displaying symptoms of foreign influence and foreign preference.
