U.S. District Court Judge Amy Berman Jackson set Manafort's trial date for September 17.
On Friday, Gates pleaded guilty to conspiracy to hide tens of millions of dollars while working with Manafort.
Manafort also said he had hoped and "expected" Gates would have had "the strength to continue the battle to prove out innocence".
Manafort attorney Kevin Downing told the court he planned to file a motion opposing the court's interpretation of a Supreme Court case referenced in her order restricting public statements in the case.
National Review contributing editor Andy McCarthy discusses former Trump campaign chairman Paul Manafort's comments against former Trump aide Rick Gates for pleading guilty to lying to the Federal Bureau of Investigation.
Manafort has pleaded not guilty to all the charges he faces, although numerous legal observers say he is under increasing pressure to strike a deal with prosecutors.
The allegations stem from much of the same conduct outlined in the Washington case, and prosecutors attempted to have all the charges brought in the pending case there.
Charlie Gile reported from Washington, and Tracy Connor from NY.
Prosecutors allege that Manafort, with Gates' assistance, laundered more than $30 million and duped banks into lending money.
On Monday, federal prosecutors moved to dismiss almost two dozen other charges that Gates faced in Virginia.
"I can understand the impulse to not let that go by without stating your innocence". In it, Manafort said Gates' decision "does not alter my commitment to defend myself against the untrue piled up charges in the indictment against me".
"I think the burden is going to fall heaviest on the defense" for trial preparations, she said.
Special Counsel Robert Mueller, who is running the Russian Federation probe, is dialing up the legal pressure on Manafort, who has not opted to cooperate with investigators.