A federal judge Friday tossed former Trump campaign chairman Paul Manafort’s lawsuit challenging the authority of special counsel Robert Mueller.

Mr. Manafort’s attorneys had asked the court to throw out all charges against him by attacking Mr. Mueller’s authority to investigate crimes unrelated to Russian election interference.

U.S. District Judge Amy Berman Jackson dismissed the lawsuit, ruling that Mr. Manafort can not use a civil lawsuit as a means to attack his criminal prosecution.

“A court should not exercise its equitable powers to interfere with or enjoin an ongoing criminal investigation when the defendant will have the opportunity to challenge any defect in the prosecution in the trial court or on direct appeal,” Judge Jackson wrote.

Mr. Manafort filed the lawsuit in January alleging that Mueller’s investigation is overly broad and not permitted under Justice Department regulations.

Last week, Kevin Downing, a defense attorney for Mr. Manafort, told Judge Jackson that his client’s activities prior the election of president Trump “have nothing to do with” Russian meddling in the 2016 election.

In the case before a federal district court in D.C., Mr. Manafort is accused of money laundering, making false statements to federal investigators and tax fraud. He has similar, but separate charges filed against him in Virginia. The allegations stem from Mr. Mueller’s investigation into collusion between the Russian government and the Trump campaign in the 2016 election. Prosecutors alleged that Mr. Manafort failed to report income from his lobbying work for the Ukrainian government in a scheme to avoid paying taxes.

He has pleaded not guilty and has maintained his innocence.

In court filings, defense counsel sought to scuttle the charges by alleging that special counsel ignored the boundaries of his jurisdiction and acted beyond the scope of his authority.

“Mr. Mueller’s actions must be set aside,” Mr. Manafort’s lawyers wrote.

Initially, defense counsel had asked Judge Jackson to dismiss all charges against Mr. Manafort. They later dropped most of that challenge, instead seeking to nullify a paragraph in Mr. Mueller’s appointment order. That order grants the special counsel the authority to “investigate any matters that arose or may arise directly from the investigation.”

In court last week, prosecutors from Mueller’s team said that Mr. Manafort’s connections to Russia-backed Ukranian politicians may have provided a “back channel” to Russia for the campaign.

Judge Jackson, who is also overseeing the criminal case, did not address the specifics of Mr. Mueller’s authority, but rather dismissed the case as Mr. Manafort using a civil suit as to wiggle out of prosecution. She said Mr. Manafort will have an opportunity to challenge Mr. Mueller’s scope during his trial.

“A civil case is not an appropriate vehicle for taking issue with what a prosecutor has done in the past or where he might be headed in the future,” she wrote.

In the civil suit, Mr. Manafort asked the court bar Mr. Mueller from bringing future charges against him. Judge Jackson said the court doesn’t have that authority because Mr. Manafort has not shown he’s in any immediate harm, noting it is not clear if Mr. Mueller will bring additional charges.

Mr. Manafort is slated to face trial in D.C., in September. A trial in Virginia is scheduled for July.

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