In late April, a lawyer for the Justice Department told a federal judge that her colleagues had been in the midst of negotiations with a Rhode Island hospital about turning over gender-transition treatment health records, only for the hospital’s lawyers to stop responding.

But Judge Mary S. McElroy of Federal District Court in Rhode Island concluded that was not true. While the government claimed it had not heard from the hospital since February, emails showed the hospital’s lawyers had stayed in close touch.

In a scathing ruling on May 14, Judge McElroy called the government’s account “misleading, if not utterly false.” At issue in Judge McElroy’s view was the “awesome power” wielded by government lawyers and the trust that they will “play fair and be honest” with courts.

The Justice Department “has proven unworthy of this trust at every point in this case,” she wrote.

The opinion was one of several heated rulings from federal judges in recent weeks castigating the government’s lawyers for withholding information and making assertions that turned out to be at odds with the facts.

A judge in Chicago said transcripts of grand jury proceedings had been redacted to hide misconduct by her district’s U.S. attorney’s office. Another judge in Rhode Island referred an assistant U.S. attorney for potential discipline after he admitted that he had knowingly withheld information from the court.

Like the one involving the Rhode Island hospital, the complaints have come as administration lawyers seek to defend major parts of President Trump’s agenda.

The government lawyers whose honesty the judges have called into question are a mix of career civil servants, political appointees and newcomers brought in as the Justice Department makes a public hiring push to fill its depleted ranks. Their missteps in court come as the department’s leadership takes an unusually combative tone with judges who rule against them, and department lawyers try to balance judges’ demands against the often stubborn posture of the executive-branch clients they represent.

But regardless, an increasing number of judges appear to be questioning the longtime assumption that Justice Department lawyers can be taken at their word, part of the “presumption of regularity” that experts say allows federal courts to operate swiftly and smoothly.

In a statement, a Justice Department spokeswoman disputed that lawyers were coming up short on ethics. “Any attack on the professionalism or integrity of D.O.J. attorneys is outrageous and unjustified,” said the spokeswoman, Natalie Baldassarre. “The department will continue to vigorously advance and defend President Trump’s agenda in federal court with the utmost respect for the institution and rule of law.”

By giving voice to their lack of trust, the judges are heralding major risk to a legal order that has been in place since Watergate. Codified in a Justice Department reference text called the Justice Manual, the basic idea is that department lawyers should be held to a higher standard because they carry with them the reputation of the entire executive branch. Before her death in 2019, Judge Patricia Wald described her expectations of the Justice Department as the “five C’s”: competence, credibility, civility, consistency and candor.

“You can’t hide the ball. You have to be honest,” said Andrew C. Mergen, who served in the Justice Department for more than 30 years under presidents of both parties and now teaches at Harvard Law School. The pattern of judges accusing department lawyers of dishonesty, he said, “is such an extraordinarily awful look for the Justice Department.”

‘The Duty of Candor’

The recent wave of rebukes surrounding courtroom honesty has come after months of clear warnings from the judiciary about separate but related concerns.

Judges have over the past year called out the administration for making dodgy legal arguments, filing dishonest testimony and failing to comply with court orders. Some of the earlier problems stem from the fact that Justice Department lawyers often represent other government agencies in court, including the Homeland Security Department, which has proved to be a difficult client, particularly in immigration cases.

But judges have taken a distinctly harsher tone in recent weeks, assigning responsibility directly to individual Justice Department lawyers for their own representations in court.

“This reckless disregard for the duty of candor owed to a federal court is appalling,” wrote Judge McElroy, referring to lawyers’ ethical obligation to never knowingly present false evidence or make false statements of fact or law. She cited recent cases in Pennsylvania, Washington and Oregon in which other judges raised questions about the government’s honesty.

The same issue arose in Chicago, where Judge April M. Perry found that Justice Department lawyers had improperly influenced a grand jury in a case in which the government was seeking indictments against four activists who were protesting outside an immigration detention facility.

Beyond the potential misconduct with the grand jury, Judge Perry found the lawyers were dishonest with her by cutting out portions of transcripts they provided her about what had unfolded. “Mistakes happen,” she said at a hearing in May. “But as I tell my children, you own it. You admit to it. You apologize for it, and you move on. What you do not do is hide it.”

In one of the Rhode Island cases, the federal bench appointed an outside counsel to investigate the head of the civil division of the U.S. attorney’s office for withholding information from her about a migrant whose case appeared before her. Judge Melissa R. DuBose said she believed the lawyer showed a “lack of candor” and that the incident represented “a serious breakdown in the ethical codes.”

In a May 22 ruling, Judge Waverly D. Crenshaw Jr. of the Middle District of Tennessee raised doubts about a former prosecutor’s claim that he — and not his bosses in Washington — had been the one to revive a criminal case against a Salvadoran man whose immigration saga is among the best known of the Trump administration’s crackdown.

Last year, the Supreme Court ordered the Trump administration to facilitate the return of that man, Kilmar Armando Abrego Garcia, to the United States after he was improperly deported from Maryland to El Salvador in what the government called an “administrative error.”

Robert E. McGuire, then the chief federal prosecutor in Judge Crenshaw’s district, told the judge that he alone made the decision to then indict Mr. Abrego Garcia on human trafficking charges stemming from a 2022 traffic stop. In fact, emails showed that Justice Department leaders in Washington stayed in close touch with him about the case, calling it a “top priority” and sending him information about a new witness after homeland security officials decided to reopen the investigation.

The judge expressed serious skepticism about Mr. McGuire’s account of his own decision-making, referring to the prosecutor’s “purported belief” and saying that he considered Mr. McGuire’s testimony, “to the extent that it is credible.”

‘It Will Get Harder’

The government’s responses to these charges have varied — an apology in the Rhode Island case before Judge DuBose, a claim in the Chicago case that there was no intent to mislead and a more combative posture in the case before Judge McElroy insisting that the government never misrepresented the facts.

In public statements, Justice Department officials have attacked “rogue judges” and “activist judges,” who they claimed were abusing their authority, and in some cases filed misconduct complaints against them. Judge DuBose and Judge Perry are appointees of President Joseph R. Biden Jr. Judge McElroy was appointed by Mr. Trump.

But Mr. Mergen, the Harvard law professor, said he has heard from career Justice Department lawyers who were demoralized by the pressures of the job, particularly the flood of petitions from immigrants challenging their detention. Pressure from the high workload, he said, was aggravated by a combination of a politicized institutional culture and judges’ growing skepticism — all of which could be contributing to the courtroom missteps.

“The risk is that the longer this goes on, the fewer good people are willing to stay,” he said. “Over time, it will get harder to do even the routine cases if judges don’t trust you.”

During prior administrations, a job as an assistant U.S. attorney was a coveted status marker for lawyers. Under the Trump administration, the department has borrowed lawyers from the Homeland Security Department and the military, posted job solicitations online and offered starting bonuses. Not only are applications down, but those who are applying are also generally less qualified, officials have said.

In an interview, Julie T. Le, a former administration lawyer who spoke out about her enormous caseload and is now running for Congress as a Democrat, said many of the difficulties she experienced arose from having to collaborate with the Homeland Security Department.

There, she said, lawyers were “used to the old way” of working in the immigration court system, which, unlike the federal courts, is under the control of the executive branch. When it came to complying with court orders, she said, “they didn’t understand. Or they understood, but they didn’t care.”

In a statement, Lauren Bis, the acting assistant secretary for public affairs at the Homeland Security Department, said its lawyers “conduct themselves with the highest integrity.” The department is not interested “in the opinions of deep state activists,” she added.

The Rhode Island case is one of several lawsuits stemming from a Trump administration effort to obtain the health records of young transgender patients in what it characterizes as an investigation into fraud.

The investigation into Rhode Island Hospital, according to the government, is being run out of the Northern District of Texas, which Judge McElroy called “a distant forum” chosen by the Justice Department because it was “friendly to its political positions.” Judge Reed O’Connor of the Texas court continues to oversee the case and has ordered Rhode Island Hospital to turn over the subpoenaed records, which will be held by the court pending the outcome of two appeals. He was appointed by President George W. Bush.

Judge McElroy also rebuked a Justice Department lawyer for telling Judge O’Connor that the department required “patient level” data, failing to note that it had settled on receiving anonymous data in other jurisdictions.

The claim that the Justice Department “needed this information,” she wrote, was “at best, deceptive, if not intentionally and knowingly false.”