Comey also kept memos from his phone conversations with Trump on at least two separate occasions, according to a source. The source says Comey wanted to keep the memos in a safe place in case they came in handy down the road. "They're preserved because he presumes someone will want to see them."

He was concerned that Trump's suggestion to end the Flynn probe could be an example of obstruction of justice . "It crossed his mind," a person familiar with the matter said, adding "even in its most benign form, it's an improper conversation. You're getting a little too close to the flame."

Comey did not share his memos with top Justice Department officials, including Attorney General Jeff Sessions and Deputy Attorney General Rod Rosenstein, despite those concerns. It was not immediately clear if he shared the memos with any staffers at a lower level.

The source says Rosenstein had not viewed the memos as of Tuesday night.

It's unclear how much the revelation of the memo factored into Rosenstein's decision to appoint Bob Mueller as special counsel of the Russia probe on Wednesday. The Justice Department declined to comment.

It is not typical for FBI directors to meet alone with the President. Justice leadership takes the lead generally on talking to administrations.

When President Barack Obama met with Comey to discuss appointing him as FBI Director, the President made clear the two would not meet one-on-one after that, according to a separate person with knowledge of the matter. "This was (Obama's) policy with the FBI director and with judicial appointees.

He felt the White House should have a clear separation from the FBI about ongoing investigations -- there should never be any intimation that the President or the White House staff was leaning in and trying to influence live investigations by the FBI," the source said.

Comey had several one-one-one meetings and phone discussions with Trump. None appeared on the White House schedule.

But Comey did meet for a dinner January 27 at the behest of the President, where sources said Trump asked if he was under investigation and sought a pledge of loyalty. The two met again on February 14, when the President kept Comey back alone after a meeting that had included Vice President Mike Pence and Attorney General Jeff Sessions. The two also spoke twice on the phone, according to Trump in an interview with Fox News.

The two also met once prior to the inauguration. At that meeting, Comey pulled the President aside to brief him on what was known about the allegations collected by a former British spy in a dossier paid for by political opponents of Trump, as CNN has previously reported.