Many Republican lawmakers, including House of Representatives Speaker Mike Johnson and Senate Minority Leader Mitch McConnell, strongly criticised the plea deals.
Khalid Sheikh 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.
Mohammed is accused of masterminding the plot to fly hijacked commercial passenger aircraft into the World Trade Centre in New York City and into the Pentagon.
The 9/11 attacks killed nearly 3000 people and plunged the US 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.