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.
One of those properties is Manafort's Manhattan apartment in Trump Tower, which Mueller said is at risk of bank foreclosure.
At another property in Fairfax, Virginia, Manafort is alleged to have acquired a mortgage "from The Federal Savings Bank through a series of false and fraudulent representations to The Federal Savings Bank." Manafort previously claimed that the property had no mortgage, Mueller said.
The special counsel is investigating whether Manafort promised to get the president of Federal Savings Bank, Stephen Calk, a job in the White House in exchange for $16 million in loans, NBC News reported Wednesday.
Manafort and Gates were indicted by the special counsel in October 2017 on multiple charges, including conspiracy to launder money, lying to federal investigators and failure to register as foreign agents in their work on behalf of a pro-Russia Ukraine party.
Manafort is a lobbyist deeply connected to the governments of Russia and Ukraine who also served as then-candidate Donald Trump's campaign chief for a time. Gates, who was Manafort's longtime associate, also worked on the Trump campaign.
Lawyers for Manafort and Gates and a spokesman for the office of the special counsel did not immediately respond to CNBC's requests for comment.