The self-styled mastermind of the 9/11 attacks and four co-defendants told a military judge at Guantanamo they wanted to confess and plead guilty.
A note to the judge said the defendants made the decision on 4 December, which was the day Barack Obama was elected to become the next US president.
Obama has said he will shut down the widely condemned Guantanamo prison camp and try detainees in the regular US civilian or military courts rather than the special Guantanamo tribunals created by the Bush administration.
Several of the defendants had said at previous hearings that they welcomed martyrdom, and they may have felt that opportunity slipping away with Obama's election.
The judge said he would question the five, including Khalid Sheikh Mohammed, who has already said he planned the Sept. 11 attacks "from A to Z," to ensure they understood the impact of their decision. All five could face the death penalty.
The judge, Army Col. Steven Henley, said he would not accept any guilty pleas during the hearings scheduled this week but did not explain why.
He read from the defendants' note, which began: "We all five have reached an agreement to request from the commission an immediate hearing session in order to announce our confessions ... with our earnest desire in this regard without being under any kind of pressure, threat, intimidations or promise from any party."
The note said all five wished to plead guilty and withdraw all pending motions filed by their military-appointed lawyers, whom they do not trust and have tried to fire.
"I am not trusting any Americans," Mohammed said in English during an appearance before the judge.
The announcement came as a surprise as the US military resumed pretrial hearings at the Guantanamo naval base, in a remote US-controlled corner of Cuba, for the accused plotters of the Sept. 11 attacks.
The judge questioned whether the law underpinning the Guantanamo tribunals allowed him to accept a guilty plea in a capital case. If the defendants are allowed to plead guilty, the case would still go through several automatic appeals, so the any death sentence would likely not be carried out for years.
The hearings went forward as scheduled, even though the pending change in the US administration made it unlikely the defendants' trials would ever be held at the base.
Mohammed, a Pakistani, and four others - Ramzi Binalshibh, Mustafa Ahmed al Hawsawi, Walid bin Attash and Ali Abdul Aziz Ali - were charged earlier this year with conspiring with al Qaeda to kill civilians.
They face 2,973 counts of murder, one for each person killed when al Qaeda militants crashed hijacked airliners into the World Trade Center, the Pentagon and a Pennsylvania field.
This week marks the fourth time the defendants have appeared before a tribunal judge at Guantanamo but there is no chance the case will be ready for trial before Obama takes office on 20 January.
Obama's transition team has met with officials from the Pentagon's Office of Military Commissions, which runs the tribunals, but details of the talks have not been made public.
In the meantime, the Pentagon is pressing forward with hearings.
"In the military that's what you do, keep moving forward to make things happen. You keep moving forward until you're ordered to do otherwise," said a spokesman for the Pentagon office that runs the tribunals, Joe Dellavedova.
The Pentagon arranged for members of five families who lost loved ones in the Sept. 11 attacks to travel to the remote Guantanamo base for the hearing, marking the first time any victims' relatives have been present at the proceedings.
They were chosen by lottery from among more than 100 who applied, said a Pentagon spokesman, Navy Cmdr. J.D. Gordon.