Calling the Trump administration’s position “disingenuous” and “troubling,” a federal judge on Saturday ordered the Pentagon to permit a lawyer for the American Civil Liberties Union to meet with a United States citizen who has been imprisoned in military custody for three months after being deemed an enemy combatant.

In a novel case pitting the individual rights of citizens against government wartime powers, Judge Tanya S. Chutkan of the Federal District Court of the District of Columbia also ordered the Pentagon not to monitor that conversation — and told it not to transfer the man, who is being held in Iraq, until the A.C.L.U. conveys his wishes to her.

A Syrian militia captured the American citizen in mid-September and turned him over to American forces as someone suspected of fighting for the Islamic State. The government has refused to identify the man, but officials familiar with the matter have said he is a dual citizen of the United States and Saudi Arabia who was born on American soil to visiting Saudi parents and raised in Saudi Arabia.

The A.C.L.U. has filed a habeas corpus lawsuit on the man’s behalf challenging his indefinite detention without charges or a lawyer. The Trump administration has asked Judge Chutkan to dismiss the case, arguing that the rights organization lacks standing to file suit on the detainee’s behalf since it has not met with the man, has no relationship with him and does not know his wishes.