A former solicitor general of the United States whose wife was killed on Sept. 11, 2001, said he was relieved to hear that a plea agreement had been reached in the case, and puzzled when the secretary of defense upended the deal.

Last week, a senior Pentagon official who oversees the military commissions signed a plea agreement with the man accused of planning the attacks and two other defendants. Then, two days later, Defense Secretary Lloyd J. Austin III rescinded it, stirring uncertainty in the case at Guantánamo Bay.

Lawyers for Khalid Shaikh Mohammed, who is accused of orchestrating the Sept. 11 plot, accused Mr. Austin in a filing on Tuesday of unlawfully breaching the plea agreement.

“I don’t think I can opine on whether the secretary of defense had the authority to do what he did,” Theodore B. Olson, the former solicitor general, said in an interview on Tuesday with The New York Times, breaking his silence on the plea deal. “But it does strike me as very unusual that someone with authority to enter into these negotiations would make a deal with these defendants and the government would turn around and renege on the deal, to abrogate the deal.”

His wife, Barbara K. Olson, 45, a conservative legal analyst, was a passenger on American Airlines Flight 77 and on her way to Los Angeles for a television appearance when the plane was flown into the Pentagon in the Sept. 11 attacks.