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.

Military defense lawyers said that although the ruling was limited to one case, they expected the issue to be raised in other cases, potentially delaying prosecutions, including the death-penalty prosecution of six detainees at Guantánamo Bay, Cuba, for the Sept. 11 attacks.

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Critics of the military commission system said Friday that the judge’s decision would provide new grounds to attack the system that they say was set up to win convictions.

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.

General Hartmann, whose title is legal adviser, has been at the center of a bitter dispute involving the former chief Guantánamo military prosecutor, Col. Morris D. Davis of the Air Force.

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.

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