A senior Pentagon official approved the deal, Defence Department officials said.
The men have been in U.S. custody since 2003, but the case had become mired in pretrial proceedings focusing on whether their torture in secret C.I.A. prisons had contaminated the evidence against them.
The plea averted a trial of as long of 18 months, or alternatively, the possibility that the military judge would throw out confessions that were crucial to the government’s case. The three men will still face a mini-trial of sorts, but probably not before next year.
Nearly 3,000 people in New York, Virginia and Pennsylvania were killed in the al-Qaeda attacks, which sparked the "War on Terror" and the invasions of Afghanistan and Iraq.
They were the deadliest assault on US soil since the 1941 Japanese attack on Pearl Harbour, Hawaii, where 2,400 people were killed.
A letter from war court prosecutors to family members of victims of the attacks said:
“These three accused have agreed to plead guilty to all of the charged offenses, including the murder of the 2,976 people listed in the charge sheet.”
