At the same time of the arraignment in U.S. District Court in Washington, D.C. a judge also will hear arguments about whether Manafort's $10 million bail should be revoked or revised as Mueller had requested last week.
If his bail is revoked, Manafort could be sent to jail while awaiting his upcoming trials. He currently is confined to home.
Manafort's lawyers last Friday called the latest indictment — which was issued the same day — "heavy-handed gamesmanship by the Special Counsel" based on "the thinnest of evidence" against Manafort
The lawyers said that Manafort's messages could not have constituted witness tampering because "he is not aware of who the Special Counsel may call as witnesses." Manafort's lawyers also argued that his right to a fair trial "may have been irreparably damaged by the Special Counsel's latest, very public and very specious" court filing.
The special counsel declined CNBC's request for comment. Manafort's lawyers did not return a request for comment.
In the new indictment, Mueller also lodged witness tampering charges against a new defendant: Manafort's Russian associate, Konstantin Kilimnik.
The indictment accuses Manafort, while being confined to his home, of conspiring with Kilimnik to influence two potential witnesses against Manafort between late February and April.
Mueller's latest salvo of charges adds to the pile of alleged criminal acts Manafort had already been accused of in the case pending in federal court in Washington.
Those existing charges include conspiracy to launder money, failing to file foreign bank account reports, acting as an unregistered foreign agent and making false statements. Manafort has pleaded not guilty to all those charges.
Manafort led Trump's presidential campaign between June and August 2016. His close associate Rick Gates, who was charged in the same federal case by the special counsel, has pleaded guilty to conspiracy against the United States and making a false statement.
Manafort is scheduled to go on trial July 24 in Virginia federal court on a related set of charges. His trial in Washington federal court is scheduled to start in September.