Attorney General William P. Barr has installed a new top deputy at the federal prosecutor’s office in Washington, raising concerns that a key U.S. attorney’s office handling multiple investigations that are of interest to President Trump is becoming further politicized.

The arrival of Associate Deputy Attorney General Michael R. Sherwin — who won the conviction of a Chinese trespasser at Trump’s Mar-a-Lago Club in Florida in September — has triggered new accusations that Justice Department leaders are bypassing career prosecutors in the office and intervening in cases favoring the president’s allies, current and former federal prosecutors in the office said.

Barr’s actions in cases handed off by special counsel Robert S. Mueller III’s Russia probe and “packing” senior supervisory positions with close associates “seriously undermines the U.S. attorney’s office in D.C.’s . . . long-standing reputation for independence from political influence,” said Charles R. Work, a former office prosecutor, Republican Justice Department political appointee and president of the D.C. Bar.

“This represents a politicization of the U.S. attorney’s office of the District of Columbia that is remarkable and unique and unprecedented,” said Stuart M. Gerson, a Republican and former Barr aide who served as acting attorney general briefly under presidents George H.W. Bush and Bill Clinton. “It’s a political coup; there really can be no question about it.”

Trump on Monday announced he intends to nominate Cleveland U.S. Attorney Justin Herdman to the office’s top slot and replace Timothy J. Shea, who has had a rocky three-month tenure. As principal assistant to Shea, Sherwin will take over the office on an acting basis effective Tuesday and can remain through mid-December without needing Senate approval. An administration official said Herdman will need Senate confirmation for the position, so it is unclear when he will arrive in Washington.

Barr selected Sherwin, a career U.S. prosecutor from Miami who specializes in national security cases, after first meeting and being impressed by him during the investigation of a deadly December shooting at a naval air station in Pensacola, Fla., officials said. Department leaders approved his move to the D.C. office after softening its sentencing recommendation for Trump political confidant Roger Stone in February. Sherwin started almost a month before Barr moved to dismiss the guilty plea of former Trump national security adviser Michael Flynn, an action no career prosecutor joined.

U.S. attorneys nationwide typically select their own top deputy, current and former prosecutors said. Although the attorney general must approve all choices, making a selection himself, and drawing from senior Justice Department leadership to do so, is unusual, they said.

The Justice Department bars active prosecutors from speaking to media outlets about cases without high-level approval. But several assistant U.S. attorneys in the office — each with experience prosecuting violent crimes or public corruption — said they felt “defanged,” torn and staggered by the personnel moves coupled with the appearance of special treatment for the president’s friends. Some said they have lost credibility when asking for cooperation from defendants, witnesses and victims whose lives depend on their word.

“How do I secure a plea now? How do I get victims to trust me? How do I get cooperators to trust me?” said one of the assistant U.S. attorneys, who each spoke on the condition of anonymity to discuss official matters.

Others said they expect defense lawyers to seek to exploit reversals and exotic rationales to block cases. Some also fear jurors in a city with pockets of grinding violence will further lose trust in the criminal justice system and will be reluctant to deliver convictions.

“Most of my defendants are people of color,” one said. “This just reinforces that belief . . . that rules that apply to them don’t apply to the affluent and well-connected.”

“We’re out here trying to hold people accountable, and you have these guys traipsing in and out of the courtroom like it’s nothing?” another marveled, referring to the president’s friends and allies.

Shea and the Justice Department declined to comment on staff members’ criticism, a spokeswoman said.

The upheaval comes as Barr has opened a criminal review of the handling of the 2016 inquiry into Trump’s campaign, and taken steps to facilitate the president’s calls to investigate his likely 2020 Democratic opponent, former vice president Joe Biden, and his family.

The U.S. attorney’s office in Washington is a traditional choice to handle such cases. The office has 300 lawyers and jurisdiction to prosecute both national security cases and political corruption across the federal government along with local and federal felonies in the District.

Accusations that Justice Department leaders were exerting control over the office were galvanized in February when Barr shifted out initial Trump appointee Jessie K. Liu as U.S. attorney before Stone’s sentencing. Liu had become a focus of Trump’s anger after a grand jury balked at indicting former acting FBI director Andrew McCabe.

Barr replaced Liu with his own counselor, Shea, as interim U.S. attorney. Shea brought in another aide of Barr’s top deputy to serve as the D.C. office’s chief of staff, and the pair immediately stumbled into a crisis in Stone’s case.

Within days, all four line prosecutors withdrew from the case when Barr undercut their sentencing recommendation for Stone, a longtime Trump political adviser who was convicted of lying to a congressional committee investigating Russian interference.

In an echo of Stone’s case, Flynn prosecutor Brandon L. Van Grack, a former Mueller team member, refused to sign the department’s April 30 motion to dismiss the former three-star general’s prosecution, according to two people familiar with the matter. Jocelyn S. Ballantine, the other line prosecutor on Flynn’s case, and John Crabb Jr., the office’s acting criminal division chief, also declined to sign, two people said.

That left Shea’s signature on the filing alone, mistakenly accompanied by Liu’s D.C. Bar identification number, as the New York Times first reported.

Flynn had admitted under oath that he lied in a January 2017 FBI interview about conversations with Russia’s ambassador related to easing U.S. sanctions.

But a federal prosecutor Barr tapped to review the case said it should be dropped because the FBI had no legitimate basis to interview Flynn, so his lies were immaterial.

Neither Van Grack, who remains with the department’s national security division as chief of a foreign lobbying disclosure and enforcement unit, nor Ballantine responded to requests for comment; Crabb declined to comment.

Sherwin approved and communicated to prosecutors the decision to give Flynn’s defense internal FBI records that the government cited in its dismissal motion, an official said. The decision to move to dismiss the case was Barr’s, and approved and communicated to Flynn prosecutors by Shea, who showed them the motion on a day’s or less notice, two officials said.

Sherwin and a spokesperson for the D.C. U.S. attorney’s office referred questions to the Justice Department, whose spokeswoman said it “does not comment on internal, deliberative conversations.”

A person familiar with the discussions who spoke on the condition of anonymity to discuss the matter said the disclosure of documents to Flynn “wasn’t because of politics, Barr or Shea. It was Sherwin as a career prosecutor saying this is the right call.”

Line prosecutors said that even if decisions came following internal discussions or disagreements, the Flynn decision has heightened concerns that office leaders are following orders from above instead of relying on subordinates’ knowledge and training in the law.

“This has knocked the wind out of us, that our office would do something like that,” one prosecutor said. “The thinking is, we have more integrity than that. . . . You file a pleading with the court and then someone sends out a tweet and it gets changed?”

Jonathan Kravis, one of four D.C. federal prosecutors who quit Stone’s case in February, called the undercutting of “career employees to protect an ally of the president an abdication of the commitment to equal justice under the law.”

Barr’s decision to further “attack” his own silenced employees “sends an unmistakable message to prosecutors and agents — if the president demands, we will throw you under the bus,” Kravis wrote.

Not all office veterans have been critical of Barr, and many remain supportive, saying the attorney general is doing his job.

Charles H. Roistacher, who served as the office’s No. 3 official under then-U.S. Attorney Joe DiGenova from 1986 to 1989, said there was nothing improper about the department’s latest actions in Stone’s or Flynn’s cases or personnel appointments.

“It is typical when you have a new U.S. attorney that supervisory positions . . . will be replaced. It happened to me,” Roistacher recalled, when DiGenova left. He lamented how politicized the office had become, but said, “The whole process [against Flynn] stunk.”

Sherwin’s supporters say he impressed Barr with his competence and not because of politics or White House connections.

Sherwin “is a career prosecutor with a stellar reputation, background and merit,” one official said.

Three Justice Department officials confirmed he was Barr’s choice to take the No. 2 slot in the district office in Washington. They cited Sherwin’s work in the investigation of the deadly December shooting at a naval air station in Pensacola, an act of terrorism that led Barr to call on Apple to unlock the shooter’s phones.

Sherwin, 48, joined the office of Barr’s top deputy in October on a 12-month detail after prosecuting a Chinese business executive who breached security while carrying a cache of electronics into Mar-a-Lago. Secret Service agents whom Sherwin interviewed introduced him to Trump, one person said. In a brief chat, Trump discussed the importance of Chinese counterintelligence work and supported the prosecution team.

Sherwin came to Washington after 13 years as a U.S. prosecutor in South Florida, eventually specializing in national security investigations. In 2011, he was asked by a deputy of Obama attorney general Eric H. Holder Jr. to serve in Afghanistan. Sherwin assisted Afghan prosecutors in conducting more than 120 criminal trials over 12 months of suspected terrorist detainees at Bagram Airfield.

Prominent Miami white-collar defense attorney David Oscar Markus, who has handled cases against Sherwin and who founded a widely followed blog about South Florida’s federal court system, called Sherwin one of only a handful of prosecutors for whom he would vouch.

“If you were looking for the person to work a case and make the right decision about it, it would be Michael Sherwin,” Markus said. “He’s a five-tool prosecutor: ethical, apolitical, smart, thoughtful, and unafraid of making the tough, but right, decision.”