The judge overseeing the prosecution of former Trump campaign chairman Paul Manafort opened Thursday’s session with an apology of sorts, saying he’d been out of line in blasting the government’s lawyers.

It was a major break for Judge T.S. Ellis III, who in little more than a week of the trial has berated prosecutors for moving too slowly through their case, limited the evidence they can present, and even accused one government lawyer of crying.

The culmination came Wednesday when Judge Ellis lost his temper with Uzo Asonye, one of the prosecutors, after learning that an IRS agent on the witness list as an expert had been sitting in the courtroom watching the proceedings all week. The judge said he thought he’d he’d made clear no witnesses were allowed to sit in on the rest of the trial, and after the prosecutors said they’d heard differently, Judge Ellis erupted.

“Let me clear, I don’t care what the transcript said … don’t do it again,” he barked, with jurors looking on.

A more contrite judge took the bench Thursday, telling jurors to ignore his outburst.

“I was critical of counsel … for allowing an expert to remain in the courtroom,” Judge Ellis said. “I may have well been wrong.”

Legal experts said the judge’s criticism of the prosecution has certainly been noticed by the jury, perhaps denting the chance for prosecutors from Special Counsel Robert Mueller’s team to sell their case that Mr. Manafort engaged in bank and tax fraud.

“I see no way that Judge Ellis‘ responses will not have an impact,” said Joshua Dressler, an Ohio State University law professor. “Judges are generally looked to with respect by jurors, so a judge’s reactions become of exaggerated importance. One would have to look at what has happened by Judge Ellis as benefiting the defense, but the extent of it can only remain to be seen.”

Lisa Kern Griffin, who teaches law at Duke University, said many judges are harsher on the government, fearing that being seen favoring a prosecution could be the basis for a defendant’s appeal. But she said the dressing downs are shaping how the jury views the prosecutors and, by extension, their case.

“The judge is getting close to tipping the scales a little too hard,” she said.

Even when the jury’s not able to hear, things are still testy.

In a private conference on Monday, as former Manafort business partner-turned-government witness Richard Gates testified, prosecutor Greg Andres complained that Judge Ellis had blocked him from asking essential questions. The judge said he was focused on moving the trial along quickly — then tore into Mr. Andres.

“Look at me when you’re talking to me,” he said to Mr. Andres.

“I’m sorry, judge, I was,” the prosecutor replied.

“No you weren’t,” Judge Ellis said. “You were looking down”

“Because I don’t want to get into trouble for some facial expression,” Mr. Andres said. “I don’t want to get yelled at again by the court for having some facial expression when I’m not doing anything, but trying my case.”

Earlier this week, Judge Ellis accused Mr. Andres of crying out of frustration during a bench conference, telling the prosecutor “there’s tears in your eyes right now.” When Mr. Andres protested, the judge shot back, “Well, they’re watery.”

Ms. Griffin said Mr. Andres is handling the repeated attacks professionally, given the judge’s authority over the courtroom.

“The best way to proceed is the way the prosecutor is doing it,” she said. “Continue to present your case, not worry about it and be deferential to the judge.”

Judge Ellis, who spent his childhood in Colombia, is a Republican appointed to the federal bench by Ronald Reagan in 1987. During his 31 years on the job, he’s handled some high profile cases including the John Walker Lindh case, the so-called American Taliban.

He showed distaste for the Manafort case early on. Even before the trial began, he accused Mr. Mueller, the special counsel probing Russian meddling in the 2016 election, of using the case as a way to gather evidence against President Trump.

“Even a blind person can see the true target of the special counsel’s investigation is President Trump, not [the] defendant,” he wrote in an early opinion this summer.

He also accused the special counsel of having unfettered power, something he sought to cure by limiting prosecutors’ references to Mr. Trump or Russian collusion in the Manafort case.

“He simply doesn’t like the case,” said Andrew Stoltmann, a federal litigator who handles white-collar case. “Judges’ real views often seep into the statements they make in front of jurors. I think that is what is happening here.”

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