The judge also allowed defendants Walid bin Attash and Ali Abdul-Aziz Ali to withdraw all their motions and go to pleas, but he refused to allow the same for two other defendants saying he had concerns over their mental competence, AFP reported.
All five face the death penalty if convicted.
Relatives look on
The note said the defendants made their decision on November 4, the day Barack Obama won the US presidential election.
|More than 200 prisoners remain held at the
Guantanamo prison camp [AFP]
Obama has said he will shut down the widely condemned Guantanamo Bay prison camp and try detainees in the regular US civilian or military courts rather than the military tribunals created by the Bush administration.
The note also said all five wished to plead guilty and withdraw any pending motions filed by their military-appointed lawyers, Henley said.
When asked by the judge if he was prepared to enter pleas Monday to all the charges should the commission allow the defendants to withdraw their motions, Mohammed, dressed in white and wearing a white turban, with a long grey and black beard, said "Yes."
"We don't want to waste time," he told the judge, speaking in English, adding that "I am not trusting any Americans".
The five defendants were watched at the tribunal proceedings by five relatives of those killed on during the 2001 attacks, in which 3000 people were killed.
Alice Hoglan, the mother of Mark Bingham, who was killed in the attacks, said she was "really proud that the commission is proceeding in its slow and thoughtful and deliberate way, despite the histrionics of these guys."
Al Jazeera's Nasser Hssaini at Guantanamo Bay said the pleas were a major victory for the US military tribunals, which have been widely condemned by international human rights groups.
Obama's opposition to the tribunals make it unlikely that they will continue after he takes office on January 20.
The US claims Mohammed confessed to masterminding the attacks and to involvement in about 30 other plots, but his lawyers say the confession was extracted by torture.
The CIA acknowledged earlier this year that Mohammed had been interrogated using the controversial "waterboarding" technique which simulates drowning.