Flynn was the first member of Trump's administration to plead guilty to a crime uncovered by special counsel Robert Mueller's wide-ranging investigation.
In February, the White House said Trump asked Flynn to resign from his position because of "eroding trust".
Trump spoke briefly to reporters as he left the White House Saturday morning - hours after Republicans passed their tax plan along party lines over night - and was asked if he was concerned what Flynn would tell the special counsel.
Some viewed Trump's comment as a straight-up "confession" to committing the crime of obstruction due to his apparent knowledge - at the time - that Flynn had not only lied to Vice President Mike Pence - but also to the Federal Bureau of Investigation.
On 'SNL,' Flynn, Putin, Billy Bush, Hillary Clinton visit Trump as Christmas ghosts
"Immediately upon learning of the allegations, the Special Counsel's Office removed Peter Strzok from the investigation", spokesman Peter Carr said.
Inspector general Michael Horowitz is leading a broader examination of the FBI's investigation of Clinton's emails.
Mueller is the only person who knows for sure what Flynn knows, he added - "but if I'm the president or one of his advisers, this just got a lot more serious". His disappointment that the FBI, one of the last agencies to lose its good standing among the American people, had succumbed to blatant partisan politics and could no longer be trusted on points of law enforcement and investigation was palpable. and heart-breaking. It is not clear what the messages said, only that they were apparently conversational responses to campaign news items and were anti-Trump and supportive of Clinton.
Feb 13: Flynn resigns over reports that he misled the White House about his contacts with Russian Federation.
As acting attorney general at the end of the Obama administration, Yates and another Justice Department official went to the White House on January 26 to warn White House counsel Don McGahn that Flynn was potentially compromised and vulnerable to blackmail because of discrepancies between the public accounting of the Kislyak conversation and what actually occurred. Mr. Trump seriously entertained the idea but ultimately backed down.
"Peter Strzok, as deputy head of counterintelligence at the FBI, was a key player in the investigation into Clinton's use of a private email server to do government work as secretary of state, as well as the probe into possible coordination between the Trump campaign and Russian Federation in the 2016 election".