In a new blow to the Bush administration’s troubled military commission system, a military judge has disqualified a Pentagon general who has been centrally involved in overseeing Guantánamo war crimes tribunals from any role in the first case headed for trial.

The judge said the general was too closely aligned with the prosecution, raising questions about whether he could carry out his role with the required neutrality and objectivity.

The judge, Capt. Keith J. Allred of the Navy, directed that Brig. Gen. Thomas W. Hartmann of the Air Force Reserve, a senior Pentagon official of the Office of Military Commissions, which runs the war crimes system, have no further role in the first prosecution, scheduled for trial this month.

Colonel Davis has said the general interfered in the work of the military prosecution office, pushed for closed-door proceedings and pressed to rely on evidence obtained through techniques that critics call torture.