A federal judge blasted the special counsel investigation of Robert Mueller Friday, accusing the former FBI director of assuming "unfettered" authority and maintaining control of the Paul Manafort prosecution solely to squeeze out incriminating information about President Trump.

And a former federal prosecutor says this was an "unprecedented rebuke" of Mueller and his team, as well as Deputy Attorney General Rod Rosenstein, who oversees the Mueller probe.

"This was a smashmouth takedown," said Joe diGenova, a former U.S. Attorney for the District of Columbia. "To question the integrity, in essence, of Mr. Mueller, because of the nature of the case that he has in front of him in federal court, is truly unprecedented."

On Friday, District Judge T.S. Ellis strongly challenged the authority Mueller and his team have to veer off into prosecuting financial crimes, such as the ones lodged against one-time Trump Campaign Chairman Paul Manafort.

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Ellis specifically wanted to know why Mueller's team had no trouble referring the Michael Cohen case to the Southern District of New York but continues to handle the prosecution of Manafort on financial allegations unrelated to Russian involvement in the 2016 campaign.

"I don't see what relation this indictment has with what the special counsel is authorized to investigate," Ellis said Friday.

"You don't really care about Mr. Manafort's bank fraud. ... What you really care about is what information Mr. Manafort could give you that would reflect on Mr. Trump or lead to his prosecution or impeachment," he added.

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Ellis also took aim at Mueller's approach to the investigation.

"What we don't want in this country, we don't want anyone with unfettered power. It's unlikely you're going to persuade me the special counsel has unlimited powers to do anything he or she wants," said Ellis.

Ellis has been on the federal bench since 1987. DiGenova says Ellis has a reputation for being a conservative but calm judge, which makes his comments on Friday all the more striking.

"I was absolutely stunned in a positive way that a judge, who was so fundamentally conservative in both his approach and his demeanor in court, was so appalled by what was happening in front of him. This is a very bad sign for Mueller," said diGenova.

"This was a remarkable dressing down for Mr. Mueller," he added.

"What it shows is that seeping out into the federal court system and judges is a sense that not only is the Mueller investigation out of control, but the supervision of it by Rod Rosenstein is either non-existent or out of control. That is a very bad sign for Mr. Mueller and Mr. Rosenstein," said diGenova.

In addition to the specifics of the investigation, diGenova says the comments from Ellis mark an important moment.

"What we are watching here is the slow education of the American people through a civics lesson, which is being conducted through the media. People are discussing the law and the Constitution and the threat to our constitutional order that the Mueller investigation represents, because it started with no crime being investigated," said diGenova.

"People are beginning to see that the original sin in the Mueller investigation was the outrageous memorandum signed by Rod Rosenstein appointing him, which mentioned no crime to be investigated," said diGenova.

DiGenova suspects the rebuke from Judge Ellis will likely quash any possibility of Mueller to subpoena President Trump.

"I don't think he's going to issue a subpoena because I think Bob Mueller knows he's going to do something then which will take him down. That will be an act of suicide. But if he is arrogant enough to do it, it will destroy his investigation. It will take him down.

"This will be the kind of stupid overreach that frequently undoes constitutional officers," said diGenova.

On Friday, Mueller's attorney, Michael Dreeben, argued that prosecuting Manafort is within the scope of the investigation based on a letter signed by Rosenstein after the investigation began. Ellis demanded to see the letter within two weeks.

DiGenova says Ellis will likely dismiss the case against Manafort if Mueller refuses to share the Rosenstein letter. Even if Ellis gets to see it, Manafort could soon get good news, given the timing of the letter.

"Remember, that letter came to Mueller from Rosenstein after the raid on Paul Manfort's home in Virginia. That could be a very serious legal problem for Mr. Mueller," said diGenova.