“No one is beyond the law in New York,” Mr. Vance said in a statement.

Mr. Vance’s position got a boost last week, when the Supreme Court ruled that criminal defendants may be prosecuted for the same offenses in both federal and state court. Since Mr. Trump’s pardon power extends only to federal crimes, the ruling leaves people he pardons subject to state prosecutions.

Mr. Manafort, who ran Mr. Trump’s 2016 presidential campaign for five months, was brought to New York a week ago to face the charges. He was indicted by a Manhattan grand jury in March.

He was brought from the Manhattan Correctional Center, a federal prison near the court, to the district attorney’s office early Thursday to formally be arrested before his arraignment in the state case.

Normally, inmates awaiting court appearances on state charges would be held in the notoriously violent Rikers Island jail complex. But Mr. Manafort was permitted to be held in the federal prison instead, after the second-highest law enforcement official in the country intervened.

In an agreement with the district attorney’s office, he will be permitted to stay in federal detention throughout the New York case.

Before a packed courtroom on Thursday, Mr. Manafort sat silently looking forward as his lawyers and an assistant district attorney, Christopher R. Conroy, conferred with Justice Maxwell Wiley about next steps. Mr. Manafort’s lawyers were given until early September to file their motions, and the next court date was set for Oct. 9.

Mr. Manafort waived his right to be present at all pretrial proceedings, likely to reduce the number of times he would have to be transported from Pennsylvania to a cell in New York. But Justice Wiley reserved the right to bring him to New York as he saw fit.