In May, President Donald Trump praised a federal judge overseeing one of Paul Manafort's criminal cases as "special" and "highly respected" because he questioned the motivation of Special Counsel Robert Mueller.

He may be regretting his words after the judge refused Tuesday to dismiss an indictment against Manafort, even as he raised concerns that a special prosecutor's probe has the potential to be politicized.

Judge T.S. Ellis III, of the Eastern District of Virginia, wrote in a footnote to a 31-page order that "a bipartisan commission with subpoena power" would be a "better mechanism" to investigate interference in the 2016 presidential election and refer crimes to the Justice Department.

But misgivings aside, Ellis said the charges against Manafort were firmly within the bounds of the order that authorized Mueller to run the election probe — including "any links and/or coordination between the Russian government and individuals associated with the campaign of President Donald Trump."

Manafort's attorneys had argued that Mueller overstepped because the charges Manafort faces in Virginia — bank fraud and failure to file tax returns related to his business dealings — have nothing to do with election meddling.

But the judge — who was appointed to the federal bench by Ronald Reagan — said it was clear that Mueller had "followed the money" paid to Manafort by pro-Russian officials to uncover the evidence outlined in the superseding indictment.

"No interpretive gymnastics are necessary to determine that the investigation at issue here falls within this category of allegations described in the August 2 Scope Memorandum," he wrote.

"Dismissal of the Superseding Indictment on the grounds urged by defendant is not warranted here," the judge wrote.

"But that conclusion should not be read as approval of the practice of appointing Special Counsel to prosecute cases of alleged high-level misconduct. Here, we have a prosecution of a campaign official, not a government official, for acts that occurred well before the Presidential election.

"To be sure, it is plausible, indeed ultimately persuasive here, to argue that the investigation and prosecution has some relevance to the election which occurred months if not years after the alleged misconduct."

But, he added, the naming of special prosecutors has the capacity to disrupt checks and balances designed to ensure no individual has too much power and "to inject a level of toxic partisanship into investigation of matters of public importance."

"Let us hope that the people in charge of this prosecution, including the Special Counsel and the Assistant Attorney General, are such people. Although this case will continue, those involved should be sensitive to the danger unleashed when political disagreements are transformed into partisan prosecutions."

Manafort also faces a separate but related indictment in federal court in Washington, where a judge revoked his bail earlier this month and tossed him in jail.