WASHINGTON — A judge at the military commission at Guantanamo Bay, Cuba, has ruled that plea bargains struck by alleged 9/11 mastermind Khalid Sheikh Mohammed and two codefendants remain valid, striking down an order by Defense Secretary Lloyd Austin to throw out the plea deals and continue to trial, a government official said Wednesday.

The official spoke on condition of anonymity because the order, by Air Force Col. and Judge Matthew McCall, has not yet been posted publicly or officially announced.

The plea agreements would spare Mohammed and two others the risk of the death penalty in exchange for guilty pleas in the long-running 9/11 case. Government prosecutors negotiated the deals with the defense under government auspices, and the top official for the Guantanamo military commission approved the deal.

The plea deals in the Sept. 11, 2001, al-Qaida attacks that killed nearly 3,000 people, spurred immediate political blowback by Republican lawmakers and others when announced in early August.

Within days of the deals becoming public, Defense Secretary Lloyd Austin issued a brief order saying he was nullifying the plea agreements. Plea bargains in possible death penalty cases over one of the gravest crimes ever on U.S. soil were a momentous step that should only be decided by the defense secretary, Austin said then.