WASHINGTON — A military appeals court has ruled against Defense Secretary Lloyd Austin’s effort to throw out the plea deals reached for Khalid Sheikh Mohammed and two other defendants in the 9/11 attacks, a U.S. official said.

The decision puts back on track the agreements that would have the three men plead guilty to one of the deadliest attacks ever on the United States in exchange for being spared the possibility of the death penalty. The attacks by al-Qaida killed nearly 3,000 people on Sept. 11, 2001, and helped spur U.S. invasions of Afghanistan and Iraq in what the George W. Bush administration called its war on terror.

The military appeals court released its ruling Monday night, according to the U.S. official, who was not authorized to discuss the matter publicly and spoke on condition of anonymity.

Military prosecutors and defense attorneys for Mohammed, the accused mastermind of the attacks, and two co-defendants reached the plea agreements after two years of government-approved negotiations. The deals were announced late last summer.

Supporters of the plea agreement see it as a way of resolving the legally troubled case against the men at the U.S. military commission at Guantanamo Bay naval base in Cuba. Pretrial hearings for Mohammed, Walid bin Attash and Mustafa al-Hawsawi have been underway for more than a decade.

Much of the focus of pretrial arguments has been on how torture of the men while in CIA custody in the first years after their detention may taint the overall evidence in the case.

Within days of news of the plea deal this summer, Austin issued a brief order saying he was nullifying them.

He cited the gravity of the 9/11 attacks in saying that as defense secretary, he should decide on any plea agreements that would spare the defendants the possibility of execution.

Defense lawyers said Austin had no legal authority to reject a decision already approved by the Guantanamo court’s top authority and said the move amounted to unlawful interference in the case.

The military judge hearing the 9/11 case, Air Force Col. Matthew McCall, had agreed that Austin lacked standing to throw out the plea bargains after they were underway. That had set up the Defense Department’s appeal to the military appeals court.

Austin now has the option of taking his effort to throw out the plea deals to the U.S. Court of Appeals for the District of Columbia Circuit. There was no immediate word from the Pentagon on any next move.