The Pentagon did not elaborate on the plea deals on Wednesday.
A US official, speaking on condition of anonymity, said the plea deals almost certainly involved guilty pleas in exchange for taking the death penalty off the table.
The September 11 attacks plunged the US into what would become a two-decade-long war in Afghanistan. (AP PHOTO)
The official said the terms of the agreement had not been publicly disclosed but acknowledged a plea for a life sentence was possible.
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 September 11, 2001 attacks on the United States.
Its population grew to a peak of about 800 inmates before it started to shrink. There are 30 inmates today.
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 September 11 attacks killed nearly 3000 people and plunged the US into what would become a two-decade-long war in Afghanistan.
His interrogations have long been the subject of scrutiny. A 2014 Senate Intelligence Committee report on the CIA's use of waterboarding and other "enhanced interrogation techniques" said that Mohammed had been waterboarded at least 183 times.
Plea deals were also reached by two other detainees: Walid Muhammad Salih Mubarak Bin 'Attash and Mustafa Ahmed Adam al Hawsawi, according to a Pentagon statement.
The three men were initially charged jointly and arraigned on June 5, 2008, and then were again charged jointly and arraigned a second time on May 5, 2012, the Pentagon statement said.
US Senate Republican Leader Mitch McConnell condemned the plea deals.
"The only thing worse than negotiating with terrorists is negotiating with them after they are in custody," McConnell said in a statement, accusing the administration of Democrat President Joe Biden of "cowardice in the face of terror".
