Acting Attorney General Matthew Whitaker speaks to state and local law enforcement on efforts to combat violent crime and the opioid crisis in Des Moines, Iowa, November 14, 2018.

Acting Attorney General Matthew Whitaker will not recuse himself from overseeing special counsel Robert Mueller's investigations despite a Justice Department ethics official recommending that he do so because of his past criticism of Mueller's probes.

Whitaker's decision leaves him with the final say over whether to challenge Mueller's major investigative or prosecutorial actions as the special counsel continues to investigate Russian interference in the 2016 presidential election, and possible collusion by President Donald Trump's campaign in that effort.

Mueller is also investigating whether Trump had obstructed justice by trying to thwart Russia-related probes. The president denies any wrongdoing.

NBC News, citing a Justice Department official, reported Thursday afternoon that Whitaker, who was appointed by Trump as acting attorney general last month, was not required to seek a formal ethics recommendation on his authority over Mueller's investigation, and did not seek such a review.

The official noted that Whitaker did not have a financial, familial or fiduciary link to a subject of Mueller's investigations.

But Whitaker did request informal advice from an ethics officer at the department.

That officer told Whitaker it was a "close call" about whether to recuse himself.

But the officer also said that if they were the attorney general, "I would recuse," according to NBC News.

That advice was based on a series of critical remarks Whitaker had made about Mueller's investigations prior to being named chief of staff to former Attorney General Jeff Sessions, who was fired last month by Trump.

Whitaker rejected that guidance.

Earlier Thursday, CNN and then NBC News had reported that Whitaker had been told by department ethics officials that he could continue to supervise Mueller. Those initial reports did not include the account that an ethics official had recommended he recuse himself.

Whitaker's previous criticisms of Mueller's probe have worried several members of Congress, who question his ability to fairly oversee the special counsel's office.

In May 2017, Whitaker told Fox News host Sean Hannity on the radio that Trump did not obstruct justice by urging then-FBI Director James Comey to drop a criminal investigation of Michael Flynn, Trump's first national security advisor. Flynn, a retired Army lieutenant general, later pleaded guilty to lying to FBI agents about his contacts with Russia's ambassador to the United States after the 2016 election.

Whitaker, while doing commentary for CNN, in August 2017 wrote an op-ed for the news site saying that Mueller's probes risked becoming a "witch hunt," a term that Trump has also used to describe the investigations. Whitaker later speculated that he could imagine a scenario in which a new attorney general who succeeded Sessions did not fire Mueller, but cut his budget by so much "that his investigation grinds to almost a halt."

The Justice Department has not responded to a request for comment by CNBC about Whitaker on Thursday.

Deputy Attorney General Rod Rosenstein, who had been overseeing the Muller probes before Whitaker's appointment, was asked at a news conference Thursday what his current role is.

"We'll have more for you on that later today," Rosenstein said. "In terms of my role, as we've described previously, we've continued to manage the investigation as we have in the past — and it's being handled appropriately," Rosenstein said.

"Whether it's Bob Mueller or Rod Rosenstein or Matt Whitaker or Bill Barr, that investigation's going to be handled appropriately by the Department of Justice."

Rosenstein was also asked whether he believed, as some congressional lawmakers have argued, that legislation should be passed to protect Mueller from being fired. He also was asked if he thought Mueller's probe is under threat.

"The investigation is being conducted in accordance with the department regulation, and nothing anybody says is going to affect that," Rosentein said.

"So I believe that that investigation is being handled appropriately under the existing department regulations."

Trump fired Whitaker's predecessor, Sessions, last month after ripping Sessions numerous times for recusing himself from the Russia probe.

Mueller, a former FBI director, was brought in by the Justice Department to handle the existing Russian inquiry after Sessions recused himself from any involvement in that probe because of his own contact with Russia's ambassador before the election while supporting Trump's candidacy.

Trump has nominated William Barr, a lawyer in private practice, to be his next attorney general. Barr, who in that position would have oversight over Mueller, previously served as attorney general under President George H.W. Bush.

Also Thursday, Senate Minority Leader Chuck Schumer, D-N.Y., called on Trump to reconsider his nomination of Barr. Schumer said Barr should not be allowed to be attorney general because he wrote an unsolicited memo to the Justice Department claiming that Mueller's obstruction of justice inquiry was based on a "fatally misconceived" theory.

"As I understand it, his theory is premised on a novel and legally insupportable reading of the law," Barr wrote in that memo this year, according to The Wall Street Journal.

"Moreover, in my view, if credited by the Justice Department, it would have grave consequences far beyond the immediate confines of this case and would do lasting damage to the Presidency and to the administration of law within the Executive branch," Barr wrote.

Schumer, in a statement Thursday, said, "Mr. Barr's memo reveals that he is fatally conflicted from being able to oversee the Special Counsel's investigation and he should not be nominated to be attorney general."

"Mr. Barr believes presidents in general — and more frighteningly, President Trump, who has shown less respect for the rule of law than any president — are above the law," Schumer said. "The fact that he holds these deeply misguided views and chose to launch them in an unprovoked written attack on the Special Counsel unquestionably disqualifies Mr. Barr from serving as attorney general again."