Michael Flynn was under FBI investigation earlier than previously thought, according to a little-noticed section in Special Counsel Robert Mueller's report -- and the former national security adviser's brother told Fox News exclusively this week that the revelation suggested a long-running, high-level effort to "trip him up" and "trap" him.

Buried in the second volume of the Mueller report was a mention of an existing FBI investigation of Flynn "based on his relationship with the Russian government," which predated Flynn's phone calls during the presidential transition in December 2016 with then-Russian ambassador Sergei Kislyak that ultimately led to his termination for lying.

It was previously thought that Flynn’s communications with Kislyak – picked up by the U.S. intelligence community – made the FBI suspicious, sparking the Flynn probe.

According to Mueller's report, "members of the intelligence community were surprised by Russia's decision not to retaliate in response to the sanctions. When analyzing Russia's response, they became aware of Flynn's discussion of sanctions with Kislyak. Previously, the FBI had opened an investigation of Flynn based on his relationship with the Russian government. Flynn's contacts with Kislyak became a key component of that investigation."

FOX NEWS EXCLUSIVE: RUSSIAN ACADEMIC SAYS HER CONTACTS WITH FLYNN WERE USED TO 'SMEAR' HIM

After Fox News reported on the development Friday morning, President Trump questioned, in a tweet, why he wasn't briefed on the probe in 2016 "so that I could make a change?"

An error occurred while retrieving the Tweet. It might have been deleted.

That section of the report cites interviews, documented in witness reports known as FBI "302s," with former acting assistant attorney general Mary McCord, who helped steer the Russia probe, and former FBI director James Comey.

"It was an absolute surprise when the Mueller report came out," Flynn's brother Joe told Fox News.

He said his brother "went through 19 sessions with the special counsel -- approximately 90 hours of torturous interviews -- and this never came up the entire time. And you would have thought it would have, and they would have maybe focused on that, but it didn't come up at all."

Joe Flynn, right, said it was an "absolute surprise" to learn that authorities had apparently been investigating his brother, Michael, during the 2016 transition or earlier. (Joe Flynn)

The special counsel's disclosure also sheds new light on a cryptic passage in the House Permanent Select Committee on Intelligence's report on Russian interference released last year. The report said Comey, in closed-door testimony, indicated there was an open case on Flynn -- which was about to be closed, until Flynn's calls with the Russian ambassador.

"Director Comey testified that he authorized the closure of the CI [counter-intelligence] investigation into General Flynn by late December 2016; however, the investigation was kept open due to the public discrepancy surrounding General Flynn's communications with Ambassador Kislyak," the report said. "Deputy Director [Andrew] McCabe stated that, 'We really had not substantiated anything particularly significant against General Flynn,' but did not recall that a closure of the CI investigation was imminent."

The same Republican report found there was no briefing to warn the Trump campaign that a senior figure like Flynn was under investigation.

"The Trump campaign was not notified that members of the campaign were potential counterintelligence concerns," even though such a defensive briefing would not have been unusual, the report said.

"My suspicion is that they were doing everything they could to trip him up and to trap him."
— Joe Flynn, on his brother Michael

"The Trump campaign," the report continued, "did not receive a general counterintelligence briefing until August 2016, and even then, it was never specifically notified about [George] Papadopoulos, [Carter] Page, [Paul] Manafort or General Flynn's Russia ties."

James Trusty, a 27-year Justice Department veteran who worked in the criminal division and served as chief of the organized crime section, told Fox News the wording in the Mueller report likely indicated the existence of an underreported investigation.

"It looks pretty clear to me that the use of the word 'previously' is suggesting an independent investigation, but there's always room for a little fog of war," Trusty said. "I think there was probably some other investigation; whether a dormant one, or a big one, a little one, we don't know, but it looks like there was something else out there."

Flynn's brother said the passage backed up the family's long-held concerns.

"Because of his vocal criticism of the Obama administration and specifically the intelligence community which he came out of, my suspicion is that they were doing everything they could to trip him up and to trap him," Joe Flynn told Fox News.

The Obama administration fired Flynn as head of the Defense Intelligence Agency (DIA) in 2014.

The Mueller report's statement concerning Flynn's Russian government contacts may have referred to a 2015 dinner in Moscow, in which Flynn sat next to Russian President Vladimir Putin and was paid $45,000 for a speech.

But Joe Flynn said his brother, who had led military intelligence, had kept colleagues in the loop.

"He did participate in an event where he made a speech over in Moscow," Flynn said. "But he briefed the DIA prior to that and he briefed the DIA after that. He maintained his top-secret security clearance right up until the point. He resigned from his job as national security adviser. So if there was a big problem with what his actions were, why wouldn't they have revoked his security clearance and told him that there's an issue here?"

Michael Flynn is still awaiting sentencing in the wake of his guilty plea for lying to investigators about conversations with the Russian ambassador. His case returned to the headlines earlier this week after prosecutors said in a court filing that Flynn had told Mueller's office that people tied to Congress and the administration tried to influence his cooperation with the probe. The judge has ordered relevant sections of Mueller's report to be unredacted. The special counsel's report did not reach a conclusion on whether the president obstructed justice, but Attorney General Bill Barr and then-deputy Rod Rosenstein determined the evidence did not warrant a criminal charge.

Former FBI general counsel James Baker, meanwhile, was recently pressed on other probes involving the Trump team before late July 2016, when the FBI opened an investigation into whether and why Trump aide George Papadopoulos had told an Australian diplomat that the Russians had dirt on Hillary Clinton.

"Just to clarify, was there an open investigation against anybody associated with the Trump campaign before this Papadopoulos investigation was opened, you know, in response to this information?" Baker was asked at the Brookings Institution.

"Not to my knowledge," Baker replied. It's not publicly known when the earlier Flynn investigation began.

Fox News asked a spokesperson for the special counsel about the Flynn investigation, including when it started, what was the predicate and whether it was separate from the FBI probe that opened in July 2016. The spokesperson declined to comment.