A judge threw out state charges against Paul J. Manafort, President Trump’s former campaign chairman, on Wednesday, dealing a setback to efforts by the Manhattan district attorney to ensure Mr. Manafort will still face prison time if Mr. Trump pardons him for his federal crimes.

Mr. Manafort had been charged in Manhattan with mortgage fraud and more than a dozen other state felonies. But Justice Maxwell Wiley of State Supreme Court dismissed the indictment, saying the charges violated the legal principle of double jeopardy, which holds that a defendant may not be tried twice for the same conduct.

The district attorney, Cyrus R. Vance Jr., had brought the charges in March 2019, shortly after Mr. Manafort was sentenced in federal court, where he was convicted of conspiracy and tax and bank fraud in two cases that had been prosecuted by the special counsel, Robert S. Mueller III.

The 16-count indictment Mr. Vance obtained from a state grand jury accused Mr. Manafort, 70, of falsifying business records to obtain millions of dollars in loans. It grew out of an investigation that began in 2017, when the Manhattan prosecutors began looking at loans Mr. Manafort received from two banks.