WASHINGTON (Reuters) - U.S. President Donald Trump’s former campaign manager Paul Manafort was dealt a setback on Tuesday when a judge who had expressed some sympathy for Manafort’s argument that a special counsel lacked the authority to prosecute him, refused to dismiss the case.

Former Trump campaign manager Paul Manafort arrives for arraignment on a third superseding indictment against him by Special Counsel Robert Mueller on charges of witness tampering, at U.S. District Court in Washington, U.S., June 15, 2018. REUTERS/Jonathan Ernst

Judge T.S. Ellis in the U.S. District Court for the Eastern District of Virginia ruled that Special Counsel Robert Mueller was properly appointed by Deputy Attorney General Rod Rosenstein in May 2017 and has the authority to prosecute Manafort.

He also disclosed that a classified August 2017 memo written by Rosenstein authorized Mueller to investigate allegations that Manafort “committed a crime or crimes by colluding with Russian government officials with respect to the Russian government’s efforts to interfere with the 2016 election.”

A spokesman for Manafort declined to comment. Russia has denied U.S. allegations of election meddling and Trump has denied campaign aides coordinated with Russian officials.

“Because the Special Counsel’s appointment was consistent with both Constitutional requirements regarding appointment of officers and statutory requirements governing the authority to conduct criminal litigation on behalf of the United States, the Special Counsel had legal authority to investigate and to prosecute this matter and dismissal of the superseding indictment is not warranted,” Ellis wrote in his opinion.

Tuesday’s ruling was the second time a judge has upheld Mueller’s prosecutorial power, which could have wide ranging implications as he investigates whether Trump’s campaign colluded with Russia.

Manafort’s argument for dismissing the case had in some ways mirrored criticism by Trump and his allies, who have sought to portray Mueller’s probe as a politically motivated “witch hunt” that was also legally out of bounds.

“This decision seems to take the wind out of those sails legally,” said Michael Zeldin, a former federal prosecutor.

Ellis is effectively saying that “it’s not an unregulated witch hunt,” Zeldin said.

Previously, Judge Amy Berman Jackson for the U.S. District Court for the District of Columbia also refused to dismiss charges against Manafort, after his lawyers sought to discredit Mueller’s probe by accusing Rosenstein of violating Justice Department rules governing the appointment of special counsels.

Manafort has been indicted in Washington and nearby Alexandria, Virginia, arising from Mueller’s investigation.

His Virginia trial starts in July and his Washington trial is scheduled for September.

Manafort has pleaded not guilty to charges including conspiring to launder money, bank and tax fraud and failing to register as a foreign agent for the pro-Russia Ukraine government.

None of the charges relate to work he performed on the 2016 campaign.

At a hearing in May, Ellis expressed skepticism about whether Mueller had the power to bring charges against Manafort.

He mused that Mueller should not have “unfettered power” and told prosecutors they were only pursuing Manafort so that he would turn over dirt on Trump.

Trump later praised the judge’s comments and read them aloud during a speech to the National Rifle Association.

In May, Ellis also demanded that prosecutors turn over to him an unredacted version of the classified August memo by Rosenstein which fleshed out the scope of Mueller’s powers, saying he needed it to inform his ruling.

In his opinion on Tuesday, Ellis said that he still has strong concerns about the use of special counsels or prosecutors more generally.

“The Constitution’s system of checks and balances, reflected to some extent in the regulations at issue, are designed to ensure that no single individual or branch of government has plenary or absolute power,” he wrote. “The appointment of special prosecutors has the potential to disrupt these checks and balances, and to inject a level of toxic partisanship into investigation of matters of public importance.”

Ellis repeated what he said in May that Trump, and not Manafort, is the target in Mueller’s sights.

“Even a blind person can see that the true target of the Special Counsel’s investigation is President Trump,” Ellis said.

Manafort has been held in a Virginia jail since the federal judge overseeing the Washington case revoked his bond on June 15 after prosecutors told a court hearing that they had evidence Manafort tried to influence witnesses’ testimony while he was under house arrest.