"I hereby ordered that defendant's motion to dismiss the superseding indictment is denied," the court ruling said.
The judge said the court has found no legal basis for Manafort's claim that Special Counsel Robert Mueller did not have authority to file criminal charges against the defendant.
The judge also determined that Mueller can investigate matters not directly related to Russia's role in the 2016 US presidential election.
Mueller in early June accused Manafort of attempted witness tampering in his fraud and tax evasion case.
Manafort still faces five other counts previously filed against him, including conspiracy against the United States, conspiracy to launder money, and failure to register as an agent of a foreign country.