A federal judge angrily accused Justice Department attorneys in newly unsealed documents of "fraud upon the court" by intimidating a witness in a case involving a former Bureau of Alcohol, Tobacco, Firearms and Explosives agent who alleges the agency trashed his reputation.

Judge Francis Allegra, who was appointed to the U.S. Court of Federal Claims in 1998 by President Bill Clinton, is presiding over a suit brought by former ATF agent Jay Dobyns against the government agency, which he claims retaliated against him and damaged his reputation. Dobyns infiltrated Hell's Angels and worked on cases involving the Aryan Brotherhood and MS-13 during his law enforcement career. 

, In a newly unsealed, Dec. 1, 2014, court ruling that legal experts said was highly unusual, Allegra accused seven Justice Department lawyers of "fraud upon the court, banned them from making any further filings in the case and took the unusual step of directly notifying Attorney General Eric Holder.

“In 40 years of legal practice, government and private, I've never seen that done,” said David Hardy, a constitutional law expert who formerly worked in the U.S. Solicitor General’s Office.

" ... a federal judge is basically questioning your candor with your court -- it’s exceedingly serious.”

- Thomas Dupree, former DOJ official

Allegra said the government attorneys may have intimidated a witness and charged that seven of them may have kept illegal behavior secret from the court.

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The controversy began after someone burned down the home of Dobyns. Dobyns claimed the ATF failed to protect his family, but the agency claimed Dobyns burned down his own home, a charge he denied. Dobyns then sued the ATF in U.S. Federal Claims Court for damaging his reputation and retaliation.

That’s when Justice Department lawyers got involved. In the ruling from last month, Allegra found a key witness in the trial said he was threatened by another ATF agent – and that ATF lawyers told the threatened agent not to tell the judge about it.

“[ATF lawyers] ordered the agent in question not to communicate the threat to the court and stated that there would be repercussions if the agent did not follow counsel’s instructions,” Judge Allegra said in his ruling.

The judge also noted that a tape recording indicates that multiple DOJ lawyers knew about misconduct and did not inform the judge.

“It’s a huge issue. Look, a lawyer’s stock and trade is his or her integrity, and to have a situation where a federal judge is basically questioning your candor with your court -- it’s exceedingly serious,” Thomas Dupree, a partner at the prestigious law firm Gibson, Dunn & Crutcher and a former DOJ official from 2007 to 2009, told FoxNews.com.

Allegra’s ruling also documents other alleged wrongdoing. When Tom Atteberry, new ATF Agent in Charge of the Phoenix office, tried to reopen Dobyns’ arson case, Justice Department attorney Valerie Baker told him not to because it would damage her defense against Dobyns. Atteberry was a witnesses in the case, but the judge didn't hear about the DOJ effort to silence him until trial. Allegra ruled that the DOJ action may amount to ‘fraud upon the court.”

“It's very, very serious,” said Dupree. “Judges don’t make allegations like this cavalierly. It's only after they have looked at the evidence and they have deep concerns that something that is not quite right. This is not by any means a run-of-the-mill, routine order.”

Last summer, Judge Allegra awarded Dobyns $173,000 in damages and rebuked the ATF for failing to adequately protect Dobyns and his family. The Justice Department appealed that ruling, but in another highly unusual move, Allegra successfully had the case remanded to his court, so he can pursue the seven government lawyers for concealing evidence. Recently unsealed documents obtained by FoxNews.com show that the DOJ disagrees with Allegra’s decision to keep the lawyers out of his court.

“[The order] limits the attorney general’s authority to select counsel to represent the United States,” a legal filing by Acting Assistant Attorney General Joyce R. Branda from Jan. 5 reads.

She added: “We are prepared to move forward with the… proceedings at the Court’s convenience.”

The judge also sent evidence of the alleged malpractice to the DOJ’s Office of Professional Responsibility, which initially opened an investigation. However, legal filings show that the agency soon suspended its investigation, saying it would wait to hear what Judge Allegra finds.

Dobyns’ lawyer said that seemed odd given that Judge Allegra had specifically asked DOJ to investigate.

“He asked OPR to investigate these matters,” James Reed, Dobyns’ attorney, told FoxNews.com. “In nearly a quarter-century practicing law I’ve never come close to seeing anything like this,” he said.

Others, such as former ATF agents, said they were not surprised given their experience with the agency.

“It is atrocious. If they can do this to a highly decorated federal agent, imagine what they can do to the average Joe,” said Vince Cefalu, a former agent who helped expose the Operation Fast and Furious scandal and who successfully sued the ATF for retaliating against him.

The ATF declined to comment on the case. Fox News also asked Attorney General Eric Holder if the lawyers involved had been disciplined. The Department of Justice declined to comment. 

Blogger David Codrea, one of the first to discover the unsealed documents, said it shows “a pattern of institutional corruption and arrogance that gets its tone set from the top.”

Maxim Lott is a Fox News Channel producer and can be reached at maximlott.com or maxim.lott@foxnews.com

William La Jeunesse joined FOX News Channel (FNC) in March 1998 and currently serves as a Los Angeles-based correspondent.