Mueller's team wanted the identities of their witnesses to remain confidential, saying in a filing last week that they haven't been criminally charged and not naming them would avoid "undue harassment."
But Judge T.S. Ellis, a Ronald Reagan appointee, said they would be identified.
He also ordered Mueller's office to provide a list of about 30 witnesses to Manafort's lawyers.
President Trump's ex-campaign chairman was in court seeking a postponement of his financial fraud trial, which is scheduled to begin Wednesday.
He also faces similar charges, and charges of witness tampering, in Washington.
Ellis said he would rule on whether to issue a delay later in the day.