WASHINGTON — A federal judge in Northern Virginia who had sharply criticized the special counsel’s case against Paul Manafort refused on Tuesday to dismiss the charges, clearing the way for Mr. Manafort to stand trial on charges of financial fraud.

Mr. Manafort, President Trump’s former campaign chairman, has been charged in two jurisdictions with a host of federal crimes as part of the special counsel inquiry into Russia’s influence on the presidential campaign.

In a preliminary hearing last month, Judge T. S. Ellis III challenged the charges of bank fraud and tax evasion against Mr. Manafort, saying he saw no relationship between the case before him and “anything the special counsel is authorized to investigate.”

But in the 31-page opinion issued on Tuesday, the judge said that “upon further review,” it was clear to him that the special counsel, Robert S. Mueller III, had “followed the money paid by pro-Russian officials” to Mr. Manafort — a line of inquiry that fell squarely in his authority.