Trump administration officials are divided over how to handle a United States citizen that the military has held in Iraq for more than three weeks as a suspected ISIS fighter, according to an official familiar with internal deliberations, raising a dilemma that could resurrect some of the biggest wartime policy questions of the post-9/11 era. Providing the first details about a predicament that the Trump administration has kept draped in near-total secrecy, the official said the problem facing Pentagon and Justice Department officials is how to ensure that the man — who surrendered on Sept. 12 to a Syrian rebel militia, which turned him over to the American military — will stay imprisoned. It may not be possible to prosecute the man because most of the evidence against him is probably inadmissible, the official said. But holding a citizen in long-term wartime detention as an enemy combatant — something the military has not done since the George W. Bush administration — would rekindle major legal problems left dormant since Mr. Bush left office and could put at risk the legal underpinnings for the fight against ISIS. Admissible evidence is sparse, said the official, who spoke on the condition of anonymity to discuss sensitive information without authorization, adding that the FBI. and Justice Department were working to build the case. Spokesmen for the National Security Council, the Justice Department and the Pentagon declined to comment on the specifics of this account but did not contest its details. But the pressure to make a decision is mounting. On Thursday, the American Civil Liberties Union filed a habeas corpus petition asking a judge to order the Pentagon to let its lawyers visit the prisoner and to rule that the government’s holding of him in detention without due process and unable to communicate is unconstitutional. “The US government cannot imprison American citizens without charge or access to a judge,” said Jonathan Hafetz, an ACLU lawyer. “It also cannot keep secret the most basic facts about their detention, including who they are, where they are being held and on what authority they are being detained. The Trump administration should not resurrect the failed and unlawful policy of ‘enemy combatant’ detentions.” But it is unclear whether the group has standing to bring that complaint without the man agreeing to let it represent him. Because Trump administration officials have refused to disclose his name, rights groups have been unable to track down any close relative to grant that assent on his behalf. The Trump administration has said almost nothing about the detainee beyond acknowledging that he exists and was recently visited by the International Committee of the Red Cross. Spokesmen at the White House, the Pentagon and the Justice Department have repeatedly demurred when asked for even basic facts about what is happening. When asked about the case at a security conference at Georgetown University on Sept. 14, two days after the suspect surrendered, John J. Mulligan, the deputy director of the National Counterterrorism Center, said he presumed that the individual would probably be charged with material support to terrorism. 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 ISIS 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 ISIS. “A US citizen may lawfully be subject to military detention in armed conflict under appropriate circumstances,” he added, pointing to a 2004 decision in which the Supreme Court upheld the indefinite wartime detention of an American citizen captured in the Afghanistan war, Yasser Hamdi. The New York Times