A panel of federal judges in New Jersey on Tuesday rejected Alina Habba’s bid to stay in the job as the state’s U.S. attorney and instead invoked a rarely used power to select a candidate of their own to take over as the state’s top federal prosecutor.

The judges announced that they had appointed Desiree Leigh Grace, an experienced prosecutor whom Ms. Habba named as her first assistant soon after she took over as interim U.S. attorney in March. The appointment is effective as of Tuesday or, alternately, upon the expiration of the 120 days of Ms. Habba’s term, according to an order signed by the district’s chief judge, Renée Marie Bumb.

That wording reflected a lack of clarity as to when Ms. Habba’s 120-day term expires. President Trump named her on March 24, saying her ascension to the post was “effective immediately” — suggesting that her term expired on Tuesday. But Ms. Habba was sworn in at the White House four days later. Counting from that date, she may still have several days in her post.

The deputy attorney general, Todd Blanche, in a social media post, suggested as much, writing that the district court judges were “trying to force out” Ms. Habba “before her term expires at 11:59 p.m. Friday.”

Apparently ignoring that the judges had indicated that they were unsure as to when Ms. Habba’s term ended, Mr. Blanche accused them of executing “a left-wing agenda.”

“When judges act like activists, they undermine confidence in our justice,” he said.

Judge Bumb was nominated by former President George W. Bush, a Republican, in 2006 and confirmed by the U.S. Senate.

The president, who selected Ms. Habba for the position and has assumed closer control of the Justice Department than any other president in the past half century, could move to fire Ms. Grace. The White House did not immediately respond to a request for comment.

A similar showdown took place last week in a federal prosecutors’ office in Albany, N.Y. There, after judges refused to extend the temporary term of John A. Sarcone III, another embattled top prosecutor appointed by Mr. Trump, the Justice Department named him “special attorney” to Pam Bondi, the attorney general.

The appointment gave Mr. Sarcone the powers of a U.S. attorney and is “indefinite,” according to a letter from the Justice Department’s human resources division that was obtained by The New York Times.

Ms. Habba, Mr. Trump’s former personal lawyer, had no experience as a prosecutor or in criminal law before the president appointed her to the temporary post.

Earlier this month, Mr. Trump nominated Ms. Habba to remain U.S. attorney permanently, but her confirmation faced headwinds in the U.S. Senate after New Jersey’s two Democratic senators said she had pursued “frivolous and politically motivated prosecutions” and “did not meet the standard” to become a U.S. attorney.

Ms. Habba is one of several of Mr. Trump’s former defense lawyers to serve in top Justice Department positions. And she has used the traditionally nonpartisan position to pursue several investigations into prominent Democrats.

Less than two months into her tenure, Ms. Habba, 41, charged Mayor Ras J. Baraka of Newark and Representative LaMonica McIver, both Democrats, after a clash with federal immigration agents outside a detention center they were seeking to tour in Newark.

Ten days later, Ms. Habba moved to drop the trespassing charge Mr. Baraka faced — a sequence of events that led a federal court judge to publicly criticize decision makers in the office. Mr. Baraka is now suing Ms. Habba for malicious prosecution.

Ms. Habba had also directed prosecutors in her office to investigate New Jersey’s Democratic governor, Philip D. Murphy, and the state’s attorney general, Matthew J. Platkin, over a policy that limits how much help local police can provide federal immigration officers.

It is not unheard-of for district court judges to appoint interim U.S. attorneys to the job permanently. That’s what happened in 2018, during Mr. Trump’s first term as president, when New Jersey judges named Craig Carpenito, then the interim U.S. attorney, as the state’s top federal prosecutor.

Across the river, in the Southern District of New York, judges voted unanimously in 2018 to install Geoffrey S. Berman as U.S. attorney. (Mr. Berman was later fired by Mr. Trump after he said he would stay in his job despite efforts by a former U.S. attorney general, William P. Barr, to remove him.)

But it is far less common for federal judges to identify a candidate on their own, even though it is authorized by a federal statute, according to Carl Tobias, a law professor at the University of Richmond.

It is striking, given Mr. Trump’s dominion over the Justice Department in his second term and his insistence on loyalty from top law enforcement officials, for a U.S. attorney to have been elevated by district judges rather than the White House. But Ms. Grace will still answer to top Justice officials in Washington.

Ms. Grace has been a prosecutor in the Newark office since 2016, according to her LinkedIn. She has risen quickly in the last five years, moving from acting chief of the office’s violent crimes unit in August 2020 to chief of the office’s criminal division in March 2024.

Ms. Habba had met with the judges who held the power to extend her term to try to persuade them of her competence.

But her efforts had largely fallen flat, according to several prominent lawyers in the state with knowledge of the discussions.