One-time Trump campaign chairman Paul Manafort keeps three US passports with different identification numbers and submitted 10 passport applications in as many years, the office of Special Counsel Robert Mueller disclosed in a new court filing on Tuesday arguing that Manafort poses a significant flight risk.

The 17-page filing came one day after Manafort and long-time business partner Rick Gates pleaded not guilty to an unsealed 12-count indictment alleging conspiracy to launder money, making false statements and other charges in connection with their work advising a Russia-friendly political party in Ukraine.

In the first criminal allegations to come from probes into possible Russian influence in US political affairs, prosecutors pressed their case against the two defendants, who face a hearing on Thursday to set bail terms. A US magistrate on Monday put the men on home confinement pending that hearing after Manafort, 68, pledged to pay a $US10 million penalty and Gates a $US5 million one if they failed to appear.

Prosecutors argued in the new filing that they "pose a risk of flight" based on a "history of deceptive and misleading conduct," the evidence against them, and their wealth and foreign connections.