The Pentagon said the plea deals had been entered into but did not elaborate on details. A US official said they almost certainly involved guilty pleas in exchange for taking the death penalty off the table.
However on Friday, Austin relieved Susan Escallier, who oversees the Pentagon's Guantanamo war court, of her authority to enter into pre-trial agreements in the case and took on the responsibility himself.
"Effective immediately, in the exercise of my authority, I hereby withdraw from the three pre-trial agreements...," Austin wrote in a memo.
Many Republican lawmakers, including House of Representatives Speaker Mike Johnson and Senate Minority Leader Mitch McConnell, strongly criticized the plea deals.
Mohammed is the most well known inmate at the detention facility in Guantanamo Bay, which was set up in 2002 by then-US President George W. Bush to house foreign militant suspects following the Sept. 11, 2001, attacks on the United States.
Mohammed is accused of masterminding the plot to fly hijacked commercial passenger aircraft into the World Trade Center in New York City and into the Pentagon. The 9/11 attacks, as they're known, killed nearly 3,000 people and plunged the United States into what would become a two-decade-long war in Afghanistan.
Plea deals had also been reached by two other detainees: Walid Muhammad Salih Mubarak Bin 'Attash and Mustafa Ahmed Adam al Hawsawi.
