Attorney General William P. Barr pushed back hard Thursday against President Trump’s attacks on the Justice Department, saying, “I’m not going to be bullied or influenced by anybody,” an assertion of independence that could jeopardize his tenure as the nation’s top law enforcement official.

The remarkable public rebuke of the president by a sitting member of his Cabinet arose from a crisis of confidence at the Justice Department, which had been accused this week of buckling to an angry tweet the president issued after learning of prosecutors’ initial prison recommendation for his longtime friend, Roger Stone.

“I think it’s time to stop the tweeting about Department of Justice criminal cases,” Barr said in an interview with ABC News, adding that such statements “about the department, about people in the department, our men and women here, about cases pending here, and about judges before whom we have cases, make it impossible for me to do my job and to assure the courts and the prosecutors and the department that we’re doing our work with integrity.”

People close to Barr said that in recent months he has become increasingly frustrated with Trump’s tweets about the Justice Department. The president, they said, seemed not only to be undercutting his own political momentum but also to be fostering doubts about the department’s independence. Trump’s tweet complaining that he believed his friend was being treated unfairly proved something of a last straw, they said, because it was so damaging to morale at the department.

Barr was comfortable not being universally loved by career employees, but he felt the tweet Tuesday raised a bigger problem, giving people reason to wonder whether the department had been corrupted by political influence and decided he could no longer remain silent about the president’s public denunciations, these people said.

Like others, they spoke on the condition of anonymity to detail private discussions within the administration.

Behind that public fight, according to people familiar with the discussions, is a deeper tension between Trump and Barr’s Justice Department over the lack of criminal charges against former FBI director James B. Comey and those close to him.

The tension has worsened in the past month, these people said, and came to a head Monday when prosecutors on the Stone case filed a recommendation to the court that Stone receive a seven- to nine-year prison sentence for his conviction on charges of obstruction of Congress and witness tampering.

On Tuesday, after Trump denounced the move, the Justice Department filed a softer sentencing recommendation, and the four prosecutors who signed the initial court filing quit the Stone case. One left the government entirely.

Barr insisted Thursday that he had planned to modify the sentencing recommendation before Trump issued his tweet but that the president’s comments made the department look bad.

Since becoming attorney general last year, Barr has enthusiastically defended the president, much to the frustration of congressional Democrats and some current and former Justice Department officials upset over what they consider an erosion of the agency’s independence. Thursday’s interview marked a stunning break from that practice.

The attorney general said he was prepared to accept the consequences of his comments.

“I cannot do my job here at the department with a constant background commentary that undercuts me,” he said. He also noted that when he became attorney general, he pledged to resist improper influence from any quarter, whether Congress, the White House or elsewhere.

The president has harshly criticized multiple current and former Justice Department officials — and a federal judge — over prosecutions and investigations involving Trump’s former associates and alleged leaking by government officials. But Barr insisted Thursday that Trump “has never asked me to do anything in a criminal case.” Trump, he said, “never” talked with him about the Stone sentencing recommendation, and he had “not discussed the Roger Stone case at the White House.”

White House press secretary Stephanie Grisham said in a statement late Thursday that the president had not lost confidence in the attorney general.

“The President wasn’t bothered by the comments at all and he has the right, just like any American citizen, to publicly offer his opinions,” Grisham said. “President Trump uses social media very effectively to fight for the American people against injustices in our country, including the fake news. The President has full faith and confidence in Attorney General Barr to do his job and uphold the law.”

The flare-up over the Stone case comes against a backdrop of growing behind-the-scenes anger from the president toward the Justice Department — more about whom the department has not charged with crimes than about whom it has charged, according to people familiar with the discussions.

Trump has repeatedly complained about FBI Director Christopher A. Wray in recent months, saying that Wray has not done enough to change the FBI’s culture, purge the bureau of people who are disloyal to him or change policies after violations of the Foreign Intelligence Surveillance Act.

He has also tweeted many times that he thinks Comey should be charged with crimes, and he was particularly upset that no charges were filed over the former FBI director’s handling of memos about his interactions with Trump. An inspector general report faulted the former director for keeping some of those memos at his home and for arranging for the contents of one of the memos to be shared with a reporter after Comey was fired in 2017.

Justice Department Inspector General Michael Horowitz referred Comey’s handling of the memos to prosecutors for possible criminal prosecution, but lawyers quickly determined it was not a close call and did not seek to build a case.

That sent Trump into a rage, according to people briefed on his comments. He complained so loudly and swore so frequently in the Oval Office that some of his aides discussed it for days, these people said. Trump repeatedly said that Comey deserved to be charged, according to their account.

“Can you [expletive] believe they didn’t charge him?” Trump said on the night of the decision, these people said. Trump has also wanted charges filed against Comey’s former deputy, Andrew McCabe. A separate inspector general investigation concluded that McCabe lied to investigators about his role in authorizing disclosures for a Wall Street Journal story in October 2016 about internal FBI tensions over an investigation of the Clinton Foundation. A grand jury in Washington seemed poised to make a decision on the case last year before fizzling into inaction.

Trump’s anger over the lack of charges against FBI personnel flared again in January, prompted by two unrelated developments, according to people familiar with the matter.

First, prosecutors updated their position in the case of former national security adviser Michael Flynn, saying a sentence of some prison time would be appropriate. Around the same time, The Washington Post reported that U.S. Attorney John Huber in Utah — tapped years earlier to reinvestigate several issues related to vague allegations of corruption against Hillary Clinton — had quietly wound down his work after finding nothing of consequence.

Those two developments further enraged the president, according to people familiar with the discussions. These people said that while the public debate in recent days has focused on leniency for Stone, the president is more upset that the Justice Department has not been tougher on his perceived enemies.

In the president’s mind, it is unacceptable that people such as Comey and McCabe have not been charged, particularly if people such as Stone and Flynn are going to be treated harshly, these people said.

In recent weeks, these people said, the president’s anger has focused increasingly on Jessie Liu, the former U.S. attorney for the District of Columbia, whose office has been handling many of the cases related to Comey and other former FBI officials.

That office has recently conducted interviews in a leak inquiry, eyeing senior FBI officials over news stories in 2017 that discussed a top-secret Russian intelligence document that influenced Comey’s decision-making in 2016. Many of investigators’ questions have seemed focused on the former FBI director.

Separately, Barr tapped U.S. Attorney John Durham in Connecticut to investigate whether any crimes were committed by FBI and CIA officials in the pursuit of allegations in 2016 that Russia interfered in the election to benefit Trump’s campaign.

After learning that the Huber investigation is not likely to produce charges, Trump has become more insistent that Durham finish his work soon, according to people familiar with the discussions. Trump, these people said, wants to be able to use whatever Durham finds as a cudgel in his reelection campaign.

All of that frustration has fed into the public fight over the Stone case.

In Thursday’s ABC News interview, Barr said that he was surprised by prosecutors’ first filing in the Stone case and that the president’s tweet had nothing to do with his decision to soften the Stone sentencing recommendation less than 24 hours after it was filed.

The attorney general said that Tim Shea, Liu’s successor as U.S. attorney for the District, had spoken with him briefly Monday, before the Stone filing, and told him the prosecutors “very much wanted to recommend the seven to nine years to the judge.” But Barr claimed that Shea told him “he thought that there was a way of satisfying everybody and providing more flexibility.”

“I was under the impression that what was going to happen was very much as I had suggested, which is deferring to the judge, and then pointing out various factors and circumstances,” Barr said.

Barr said when he saw news reports Monday night of the recommendation that was filed, he thought, “Gee, the news is spinning this; this is not what we were going to do.”

“I was very surprised,” Barr said. “And once I confirmed that that’s actually what we filed, I said that night, to my staff, that we had to get ready because we had to do something in the morning to amend that and clarify what our position was.”

Next came the president’s tweet complaining that Stone was being treated unfairly, which Barr said put him in an untenable position.

“Once the tweet occurred, the question is, ‘Well, now what do I do?’ ” Barr said. “And do you go forward with what you think is the right decision, or do you pull back because of the tweet? And that just sort of illustrates how disruptive these tweets can be.”

Barr said Trump would be within his rights to ask for an investigation in an area that didn’t affect his personal interests — such as in a terrorism case, or fraud by a bank. But he said an attorney general would not listen to an order to investigate a political opponent.

“If he were to say go investigate somebody, and you sense it’s because they’re a political opponent, then an attorney general shouldn’t carry that out, wouldn’t carry that out,” Barr said.

On Wednesday, Trump praised the department’s change of course and singled out Barr specifically.

“Congratulations to Attorney General Bill Barr for taking charge of a case that was totally out of control and perhaps should not have even been brought,” Trump wrote on Twitter. “Evidence now clearly shows that the Mueller Scam was improperly brought & tainted.”

People close to Barr said that the tweet of praise frustrated the attorney general because it further cemented the public notion that the attorney general was doing Trump’s bidding on the Stone case.

Democrats called this week for the Justice Department inspector general to investigate the dispute surrounding Stone’s sentence recommendation.

Stone was convicted by a jury in November. The charges against him were the last filed by former special counsel Robert S. Mueller III as part of his investigation of Russian interference in the 2016 presidential election.

The new sentencing recommendation — signed by Shea and a different career prosecutor — said the previous guidance “could be considered excessive and unwarranted under the circumstances.” Shea, a former close adviser to Barr at Justice Department headquarters, was installed at the U.S. attorney’s office in the District last month.

Prosecutors and defense lawyers can only make recommendations about prison sentences. Stone’s sentencing is scheduled for Feb. 20 before U.S. District Judge Amy Berman Jackson, whom Trump also targeted this week in tweets complaining about her treatment of Paul Manafort, his former campaign chairman, and suggesting Jackson had, in another case, gone too easy on his Democratic rival in 2016, Hillary Clinton.

Separately on Thursday, Chief U.S. District Judge Beryl A. Howell of Washington also issued a rare statement responding to President Trump’s attacks on Jackson.

“The Judges of this Court base their sentencing decisions on careful consideration of the actual record in the case before them; the applicable sentencing guidelines and statutory factors; the submissions of the parties, the Probation Office and victims; and their own judgment and experience,” Howell said. “Public criticism or pressure is not a factor.”

Spencer S. Hsu contributed to this report.