Flynn, a retired Army general, has always been of interest to the Federal Bureau of Investigation and Mueller, the Department of Justice special counsel.
Flynn resigned as national security adviser after 24 days following reports that he had misled Vice President Mike Pence about a call with a top Russian official regarding USA sanctions on the country.
"It depends on what the president has done and what the president's conversations with Michael Flynn and others have been", Bharara told CNN's "State of the Union" when asked if Trump should be concerned.
Pressure on Flynn to cooperate with investigators increased after prosecutors began focusing on his son, Michael G. Flynn, ABC News reported, citing sources familiar with the investigation.
Flynn is facing federal, congressional, and military investigations into undisclosed payments from foreign governments, including Russian Federation and Turkey.
The elder Flynn has also been of interest to congressional investigators, who are running their own probes into the Russian meddling and possible collusion. He has continued to do so even after Mueller's announcement of the first criminal charges stemming from the inquiry. "Where's the Flynn piece?" he said.
Flynn's attorney's had been sharing details with Trump's lawyers about the investigation by the special counsel before pulling away. "No one should draw the conclusion that this means anything about General Flynn cooperating against the president", Trump lawyer Jay Sekulow told reporters in a statement. "The reason why you would pull out of that is because your interests are no longer aligned".
The New York Times was the first to report on the split between the Trump and Flynn teams. "Also, prosecutors accept cooperation only if you can provide "substantial assistance". Stay tuned", he added, in a comment that was echoed by a former White House Special Counsel for Ethics who said Flynn would only be cooperating with Mueller if he had something on Trump. Peter Carr, a spokesman for the special counsel, declined to comment on the ongoing investigation.