A decision by a military judge on Friday to disqualify a top Pentagon official from any further role in a Guantánamo war crimes case was a major new challenge to the Bush administration’s legal approach to the war on terrorism.

The ruling, in the case against Salim Hamdan, a detainee who was a driver for Osama bin Laden, transformed what had been something of a Pentagon soap opera over how to prosecute detainees into a formal ruling that gave new force to critics’ accusations of improper political influence over this country’s first use of military commissions since World War II.

At issue is the role of a Pentagon office called the “convening authority,” which oversees the military prosecutors and has extensive power over the defense lawyers and judges in the cases against Guantánamo detainees. One role of that office is to be a neutral arbiter, deciding such matters as allocation of resources for both the defense and prosecution and which charges brought by prosecutors should go to trial.

But military defense lawyers and other critics have said officials running that office have overstepped the bounds of impartiality by pushing prosecutors to charge more detainees and to use evidence obtained under coercive interrogations.