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Paul J. Manafort, President Trump’s former campaign chairman who is serving a federal prison sentence, had been expected to be transferred to the notorious Rikers Island jail complex this month to await trial on a separate state case.

But last week, Manhattan prosecutors were surprised to receive a letter from the second-highest law enforcement official in the country inquiring about Mr. Manafort’s case. The letter, from Jeffrey A. Rosen, Attorney General William P. Barr’s new top deputy, indicated that he was monitoring where Mr. Manafort would be held in New York.

And then, on Monday, federal prison officials weighed in, telling the Manhattan district attorney’s office that Mr. Manafort, 70, would not be going to Rikers.

Instead, he will await his trial at a federal lockup in Manhattan or at the Pennsylvania federal prison where he is serving a seven-and-a-half-year sentence for wide-ranging financial schemes, according to people with knowledge of the matter.