The charges, first reported by Politico, were put under seal by Judge Amy Berman, keeping details about the charges themselves from public view.
The development follows the special counsel's recent discovery of alleged "additional criminal conduct" articulated in a court document sent from the prosecutor's office Friday.
In that filing, Manafort and Gates were accused of "a series of bank frauds and bank fraud conspiracies." Some of those bank frauds are related to properties that Manafort is seeking to pledge as collateral in lieu of a $10 million bail bond, the special counsel said.
Mueller's office said the three properties Manafort put up for bail are insufficient substitutes for the bond.
"The bail package that Manafort proposes is far less than the $10 million that he alleges in his supplemental memorandum, and the difference is not made up by any surety," the special counsel said.