The 2008 conviction of Osama bin Laden’s media secretary in a military commission at Guantanamo Bay, Cuba, must be vacated because of a ruling by a federal appeals court in another terrorism case, the Justice Department said in a court filing Wednesday.

But the government said that the court decision that requires overturning the conviction is flawed and that the Justice Department may appeal to the full court of appeals or the Supreme Court.

In October, a panel of the U.S. Court of Appeals for the District of Columbia Circuit threw out the conviction of bin Laden’s driver, Salim Hamdan. The judges found that the charge on which he was prosecuted — providing material support for terrorism — was not a war crime at the time of his offense.

The reasoning in the Hamdan case forced the appeals court to strike down the conviction of Ali al Bahlul, a Yemeni propagandist for al-Qaeda who was convicted of material support, conspiracy to commit war crimes and solicitation to commit war crimes, the government said.

Conspiracy and solicitation also were not recognized as international war crimes when Bahlul and other detainees committed the alleged acts, the government acknowledged. In 2006, Congress included them in the Military Commissions Act. The Justice Department said that Congress intended detainees to be prosecuted for those offenses for conduct committed before 2006 and that the court erred in concluding that there was no such authorization in the act.

The Justice Department did not explicitly say it would appeal, and there has been debate within the government about whether to drop material support and conspiracy charges to burnish the legal standing of military commissions. That debate was first described in the New York Times.

“I would have thought if the government had decided to take this to the Supreme Court, the language in the brief would be stronger,” said Stephen I. Vladeck, a law professor at American University. “Part of that may reflect continued debate in the administration about how best to proceed.”

If the charges of material support and conspiracy were abandoned, that would probably reduce the number of additional cases that could be brought against alleged low-level fighters held at the detention center in Cuba — those who may have been involved with al-Qaeda but cannot be tied to a specific terrorist act.

The legal dispute will have minimal impact on the death penalty case against Khalid Sheik Mohammed, the self-proclaimed mastermind of the Sept. 11, 2001, attacks, and his four co-defendants.

After Wednesday’s filing, Gen. Mark Martins, the chief military prosecutor at Guantanamo Bay, recommended that the charge of conspiracy be withdrawn against Mohammed and the others. But seven other charges remain, including murder in violation of the law of war, attacking civilians and hijacking aircraft.

“There is a clear path forward for legally sustainable charges,” Martins said in a statement. “The remaining charges are well-established violations of the law of war and among the gravest forms of crime recognized by all civilized peoples. This action helps ensure the prosecution proceeds undeterred by legal challenge.”

Conspiracy would have been a viable charge against Bahlul — and by extension, others — in federal court, but Congress has barred the use of civilian criminal trials to prosecute Guantanamo detainees.

Bahlul’s attorney declined to comment on Wednesday’s filing. If his conviction is vacated, Bahlul, who is serving a life sentence, will be returned to the general population at Guantanamo. The government argues that it can continue to hold him and other detainees without trial under the laws of war and subject to review in federal court. While individual detainees have won their release in U.S. District Court, federal judges have upheld the government’s power to detain others.

Hamdan, whose conviction triggered this latest round of litigation, was returned to Yemen in 2008.

Julie Tate contributed to this report.