Flynn stepped down amid revelations he misled administration officials about discussions he had with Russia’s U.S. ambassador.
“We have taken the administrative step of suspending Mike Flynn’s access to classified information pending a review,” Defense Intelligence Agency (DIA) spokesman James Kudla said.
“We take this standard administrative action when questions arise concerning an individual’s compliance with security clearance directives.”
The DIA has been the custodian of Flynn’s security clearance since his time there as director from 2012 to 2014. A security clearance is not necessarily tied to a position, but generally a period of time, meaning individuals such as Flynn can retain their clearance after resignation.
Federal government guidelines on classified information state “foreign influence” as a security concern that could prompt the revocation of a clearance.
“Foreign contacts and interests may be a security concern if the individual ... is vulnerable to pressure or coercion by any foreign interest,” state the guidelines.
ABC News has previously reported that the Department of Justice contacted the White House in January with its concerns that Flynn had misled the administration about his contact with Russian Ambassador to the U.S. Sergey Kislyak, and was potentially vulnerable to blackmail.
Flynn's communications with the ambassador included discussing U.S. sanctions imposed on Russia over its involvement in the 2016 U.S. presidential election.
In his resignation letter, Flynn wrote that he “inadvertently briefed the vice president-elect and others with incomplete information regarding my phone calls with the Russian ambassador.”
Tuesday, White House Press Secretary Sean Spicer said that the "level of trust between the President and General Flynn had eroded to the point where [the president] felt he had to make a change."
In a press conference Wednesday at the White House, President Trump called Flynn a "wonderful man" who had been treated "very, very unfairly by the media, as I call it, 'the fake media' in many cases."