The FBI’s investigation into Russian interference in the presidential election is on uncertain footing after President Trump abruptly fired the man leading it, Director James Comey.

Agents were reportedly floored by the dismissal, and some are wondering whether they will be allowed to continue that probe, according to a report in The New York Times.

Multiple media outlets reported Wednesday that Comey had sought significant additional resources for the investigation just days before he was fired, suggesting an intensifying inquiry.

The Justice Department flatly denied the reports, calling them “totally false.”

Perhaps most transparently, critics say, the president himself seemed to hint that his motivation for firing Comey was displeasure with the investigation into whether Trump campaign associates coordinated with Russia to help swing the election in his favor.

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“While I greatly appreciate you informing me, on three separate occasions, that I am not under investigation, I nevertheless concur with the judgment of the Department of Justice that you are not able to lead the Bureau,” Trump wrote in the second paragraph of his Tuesday letter axing Comey.

The White House has insisted that the impetus for firing Comey came from Deputy Attorney General Rod Rosenstein and was grounded in his concerns with Comey’s handling of the investigation into Hillary Clinton Hillary Diane Rodham ClintonBarr criticizes DOJ in speech declaring all agency power 'is invested in the attorney general' Virginia Democrat blasts Trump's 'appalling' remark about COVID-19 deaths in 'blue states' The Hill's Campaign Report: Biden asks if public can trust vaccine from Trump ahead of Election Day | Oklahoma health officials raised red flags before Trump rally MORE’s use of a private email server while secretary of State.

Yet the White House said Wednesday that Trump had been weighing Comey’s ouster since day one of his presidency.

Some former FBI officials are skeptical and see the move as a crudely disguised effort to strangle the Russia investigation, which appeared to be accelerating.

“What I found most odd was, [given] the extent to which they were trying to use the misconduct around the Clinton investigation as the justification, Trump mentioning the Russia investigation in his dismissal letter was what in law enforcement we call a ‘clue,’ ” said Michael German, a former FBI special agent, with a chuckle.

The White House has repeatedly downplayed the probe in the midst of the media firestorm that followed the shocking announcement that Comey was out.

White House spokeswoman Sarah Huckabee Sanders, speaking of the FBI investigation, described it as “probably one of the smallest things they’ve got going on their plate.”

The night before, in an interview with Fox News’s Tucker Carlson, Sanders had talked of the need to move on from the Russia probe.

Former officials say that career investigators — who take pride in the political independence of the bureau — will continue to work the case, at least for now.

In the hours after Comey’s dismissal, according to ABC News, acting FBI Director Andrew McCabe held a call with offices across the country and delivered the message: “Business as usual.”

“It shouldn’t get impacted at all,” said Ron Hosko, a former assistant director at the bureau. But, he said, “What we will have to be alert for, is there some question about how the investigation is being supported by [Justice Department] prosecutors?”

The news of Comey’s dismissal was a shock to agents at the bureau, where Hosko and others say he enjoyed broad support — even among those who disagreed with his decisions in the Clinton case.

Sanders on Wednesday claimed that “the rank-and-file” agents had lost confidence in Comey, an assessment that was met with raised eyebrows in Washington.

“I don’t buy that. I was with people last night from the bureau. I was not hearing that,” Hosko said. “I think broadly he was respected, liked, trusted.”

Although he was deeply controversial at times, Comey was a vociferous and habitual defender of the men and women who work at the FBI. Perhaps the only time he became heated when giving public testimony before Congress was when the integrity of the bureau was questioned.

“You can call us wrong, but don’t call us weasels. We are not weasels,” Comey famously declared at a House Judiciary Committee hearing in September.

It’s unclear who will replace Comey and inherit the politically explosive probe.

With Comey gone, the investigation is now temporarily under McCabe’s command until an interim director is chosen. He is under consideration for the role, a Justice Department official told The New York Times.

Attorney General Jeff Sessions Jefferson (Jeff) Beauregard SessionsTrump's policies on refugees are as simple as ABCs Ocasio-Cortez, Velázquez call for convention to decide Puerto Rico status White House officials voted by show of hands on 2018 family separations: report MORE and Rosenstein also reportedly interviewed four other candidates on Wednesday: William Evanina, the director of the National Counterintelligence and Security Center at the Office of the Director of National Intelligence; Paul Abbate, assistant director of the bureau’s cyber branch; and two field office heads: Michael Anderson in Richmond, Va., and Adam Lee in Chicago.

That person will lead the bureau until a permanent director is confirmed by the Senate Judiciary Committee — likely to be a bruising media frenzy no matter whom the administration taps.

The White House has given few signals about any potential leads.

Speculation has swirled around McCabe, former House Intelligence Committee Chairman Mike Rogers (R-Mich.), former FBI Deputy Director John Pistole and New Jersey Gov. Chris Christie (R).