In a sharp rebuke of those claims, Judge Amy Berman Jackson of US District Court for the District of Columbia ruled that Deputy Attorney General Rod Rosenstein had followed all the Justice Department's rules when he hired Mueller and Mueller's case against Manafort is not overly broad or improper.
Rosenstein "expressly approved the Special Counsel’s investigation of the facts alleged in the indictment, so there has been no violation of the regulations, and the Special Counsel did not act without authority," wrote Jackson, who was appointed by Democratic President Barack Obama.
In response to the ruling, Manafort spokesman Jason Maloni said: "Paul Manafort maintains his innocence and looks forward to prevailing in this matter." A spokesman for the Special Counsel declined to comment.
Manafort, who performed lobbying work for a pro-Russian former Ukrainian president before serving as Trump’s campaign chairman in 2016, is facing two indictments brought by Mueller in federal courts in Washington and Alexandria, Virginia.
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The charges against him in the Washington case include conspiring to launder money, conspiring to defraud the United States and failing to register as a foreign agent. In Virginia, he faces charges that include bank fraud and filing false tax returns.
He has pleaded not guilty to all of the charges, none of which are directly related to work he performed for Trump's campaign.
In both criminal cases, Manafort has asked the courts to dismiss the charges on the grounds that Rosenstein's May 17, 2017 appointment order hiring Mueller runs afoul of Justice Department rules on special counsels.
He has also argued that Mueller's case against him has nothing to do with Russian interference in 2016 election, and that the probe by the FBI into his Ukraine dealings predates the Russia probe.
Trump has denied that his campaign colluded with Russia and called the probe that has dogged his presidency a "witch hunt."
Jackson was not moved by any of Manafort's assertions.
"Manafort was, at one time, not merely 'associated with,' but the chairman of, the Presidential campaign, and his work on behalf of the Russia-backed Ukrainian political party and connections to other Russian figures are matters of public record," she wrote, adding that it was "logical" for investigators to probe Manafort's dealings.
Her ruling also pointed to an August 2017 memo by Rosenstein that further detailed the scope of the probe. That memo explicitly gave Mueller authority to probe all of Manafort's Ukraine-related work predating the 2016 campaign.
Republicans in the House of Representatives who are critical of the Mueller probe have pressed the Justice Department in recent months to provide them with an unredacted copy of the August memo.
The ruling marks a setback for Manafort, who last month was buoyed when the judge in the Alexandria case aggressively questioned prosecutors about whether their case was overly broad and mused that he believed they were using the charges to get Manafort to turn over dirt on Trump.
That judge, TS Ellis III for the Eastern District of Virginia, has yet to rule on whether to dismiss the charges against Manafort.
Ellis, who was appointed to the bench by Republican President Ronald Reagan, has also said he too wants to see an unredacted copy before he can fully form a decision on whether to dismiss the charges.
He told prosecutors to turn over a copy to him by Friday.
