The senior administration official partly opened a window onto the matter. The prisoner, the official said, was born on American soil, making him a citizen, but his parents were visiting foreigners and he grew up in the Middle East. The near total lack of contact with the United States slowed efforts to verify his identity, the official said.

The prisoner was interrogated first for intelligence purposes — such as to determine whether he knew of any imminent terrorist attacks — without being read the Miranda warning that he had a right to remain silent and have a defense lawyer present. The government then started a new interrogation for law-enforcement purposes, but after the captive was warned of his Miranda rights, he refused to say any more and remains in military custody in Iraq, the official said.

Investigators have also identified a personnel file in a cache of seized Islamic State documents that appears to be about the captive, the official said. But prosecutors could have difficulty getting that record, which was gathered under battlefield conditions, admitted as evidence against him under more rigorous courtroom standards.

As a result, while the Pentagon wants the Justice Department to take the prisoner off its hands, law enforcement officials have been reluctant to take custody of him unless and until more evidence is found to make it more likely that a prosecution would succeed, the official said.

There is a limit to how long the military can hold a citizen without at least letting him talk to lawyers, said Stephen Vladeck, a law professor at the University of Texas, Austin, who specializes in national security matters, acknowledging the government’s predicament.

“It would be one thing if this were a cooperating witness who was being kept in incommunicado detention to protect his safety and his intelligence value,” Mr. Vladeck said. “But keeping someone in these circumstances simply because they don’t know what to do with him is not going to help them in court, if and when it gets there.”

The Pentagon spokesman, Maj. Ben Sakrisson, said that “captured enemy fighters may be detained” as part of the armed conflict against the Islamic State.