WASHINGTON — An American citizen who has been held in military custody in Iraq for 11 weeks refused to talk to F.B.I. interrogators without a lawyer after he was warned of his Miranda rights to remain silent and have a lawyer present, the Justice Department told a federal judge on Thursday.

“The individual stated he understood his rights, and said he was willing to talk to the agents but also stated that since he was in a new phase, he felt he should have an attorney present,” the department said in a court filing Thursday afternoon. “The agents explained that due to his current situation, it was unknown when he would be able to have an attorney, and the individual stated that it was O.K. and that he is a patient man.”

The filing came in response to an order by Judge Tanya S. Chutkan of the Federal District Court of the District of Columbia, after a contentious hearing earlier on Thursday during which she warned that the Trump administration seemed to be claiming “unchecked power that is, quite frankly, frightening.”

The case centers on an American who was captured by a Syrian militia in mid-September, apparently fighting for the Islamic State, and turned over to American military forces. Although the International Committee for the Red Cross has visited the detainee twice, the government has kept secret even the most basic facts about him, including his name.