The decision was a setback for Paul Manafort in his defence against charges of money-laundering conspiracy, false statements and acting as an unregistered foreign agent.
Mr Manafort, who performed lobbying work for a pro-Russian former Ukrainian president before serving as Mr Trump's campaign chairman in 2016, is facing two indictments brought by Mr Mueller in federal courts in Washington and Alexandria, Virginia.
Jackson said the Manafort prosecution falls squarely within the mandate of Mueller, whose May 2017 appointment order directs him to investigate links or coordination between Russian Federation and people associated with Trump's campaign. A spokesman for the Special Counsel declined to comment.
Manafort has pleaded not guilty to all of the charges, none of which are directly related to work he performed for Trump's campaign. He has also argued that Mr Mueller's case against him has nothing to do with Russian interference in 2016 election, and that the probe by the Federal Bureau of Investigation into his Ukraine dealings predates the Russia probe. And Donald Trump cited them in a speech to the National Rifle Association to claim that Mueller's indictment is a "phony Russian Federation witch hunt".
As Judge Jackson explains, Manafort's challenge to Mueller's authority fails for four reasons. "It was logical and appropriate for investigators tasked with the investigation of "any links" between the Russian government and individuals associated with the campaign to direct their attention to him".More news: Fortnite gets new burst assault rifles in tomorrow's patch
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Her ruling also pointed to an August 2017 memo by Mr Rosenstein that further detailed the scope of the probe.
The former campaign manager for President Trump is being charged in Washington D.C. with failing to register as a lobbyist while working in Ukraine.
That judge, T.S. Ellis, said he believed prosecutors were using the charges against Manafort to try to get him to turn against Trump.
In response to these charges, Manafort claimed that he could not be prosecuted by Special Counsel Robert Mueller because the particular charges against him are outside of Mueller's properly delegated authority.
Second, even if Mueller had exceeded his authority, the regulations governing appointments of special counsel provide that they "are not meant to, do not, and may not be relied upon to create any rights, substantive or procedural, enforceable at law or equity, by any person or entity, in any matter, civil, criminal, or administrative".