The official spoke on condition of anonymity because the order by the judge, Air Force Col. Matthew McCall, has not yet been posted publicly or officially announced.
The plea agreements would spare Mohammed and the others the risk of the death penalty in exchange for guilty pleas in the long-running 9/11 case. Government prosecutors had negotiated the deals with defense attorneys under government auspices, and the top official for the military commission at Guantanamo Bay, Cuba, had approved them.
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 late July.
The agreements, and Austin's attempt to reverse them, have been one of the most fraught episodes in a U.S. prosecution marked by delays and legal difficulties, including years of ongoing pretrial hearings to determine the admissibility of statements by the defendants given their years of torture in CIA custody.
Within days of the deals becoming public this summer, Austin issued a brief order saying he was nullifying them. Plea bargains in possible death penalty cases tied to one of the gravest crimes ever carried out on U.S. soil were a momentous step that should only be decided by the defense secretary, Austin said at the time.
The Pentagon is reviewing the judge's decision and had no immediate further comment, said Maj. Gen. Pat Ryder, Pentagon press secretary.
The New York Times first reported the ruling.
Military officials have yet to post the judge's decision on the Guantanamo military commission's online site.
However, a legal blog that long has covered the prosecutions from the Guantanamo courtroom said McCall's 29-page ruling concludes that Austin lacked the authority to toss out the plea deals.
The ruling also calls the timing of Austin's move "fatal," coming after Guantanamo's top official already had approved the deals, according to the blog, called Lawdragon.