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Attorney General Eric H. Holder Jr. decided to press forward with the case, fighting the appeal of a guilty verdict against the prisoner, a Yemeni man named Ali al-Bahlul. In an unusual move, Mr. Holder overruled the recommendation of the solicitor general, Donald B. Verrilli Jr., who had wanted to drop the case because the appeals court had rejected the same legal arguments in another case several months ago, according to officials familiar with the deliberations.

The chief prosecutor of the military commissions system, Brig. Gen. Mark Martins, had also urged the Justice Department to drop the case and pointedly did not sign the 22-page brief to the court on Wednesday. It concedes that the judges must side with Mr. Bahlul at this stage because of the earlier ruling in the other case, but argues that the earlier ruling was wrong.

General Martins also announced on Wednesday that he was abandoning the conspiracy charge in the death penalty case against Khalid Shaikh Mohammed and four others accused of being accomplices in the terrorist attacks of Sept. 11, 2001.

"There is a clear path forward for legally sustainable charges," he said. "The remaining charges are well-established violations of the law of war and among the gravest forms of crime recognized by all civilized peoples."

The current dispute traces back to two tribunal trials from 2008. In October, the appeals court vacated the conviction of the defendant in the first case, a former Al Qaeda driver who is now free in Yemen, because his charge, material support, was not an international war crime. It rejected the government's argument that such a charge was valid under an "American common law of war."

It was after that ruling that General Martins urged dropping the case against Mr. Bahlul, a producer of Al Qaeda propaganda videos who is serving a life sentence. General Martins held that fighting a protracted legal battle with arguments that had already lost would damage the tribunals' legitimacy.

He was backed by the top lawyers at the Pentagon and the State Department, Robert Taylor and Harold Koh. But Lisa Monaco, the assistant attorney general for national security, argued that the "American common law of war" theory might win at the Supreme Court, officials said.

The administration's latest move leaves it to the judiciary to decide whether to remove conspiracy and material support from the offenses available for trial before tribunals. Without such charges, which make it easier to prosecute people who participated in Al Qaeda but are not linked to a specific attack, fewer Guantánamo detainees can receive tribunal trials. Congress approved the inclusion of both charges in laws enacted in 2006 and 2009.

Mr. Holder had once sought to prosecute the Sept. 11 case in a civilian court instead of a tribunal, but the White House overruled his plan in 2010 amid an uproar over security.