Mohammed, who has previously said he conceived and orchestrated the Sept. 11 attacks, gave no reason for wanting to sit out the hearing but on Monday dismissed the military tribunal with scorn, saying "I don't think there is any justice in this court."
Authorities have portrayed the other defendants as Mohammed's underlings, who provided logistical and other help to the Sept. 11 hijackers. All five face the same charges, which include terrorism and murder, in what is considered one of the most significant terror prosecutions in U.S. history. They all could get the death penalty if convicted at a trial that is at least a year away.
Saudi defendant Mustafa Ahmad al-Hawsawi and Pakistani national Ali Abd al-Aziz Ali, a nephew of Mohammed, also chose to boycott the hearing. Neither provided any reason for their absence but a lawyer for al-Aziz Ali had said on Monday that his client's father had recently died in Kuwait and he was grieving for him.
Those who showed up in court, for the second day in a weeklong pretrial hearing, were Walid bin Attash, a Yemeni who grew up in Saudi Arabia, and Ramzi Binalshibh, another Yemeni who was originally chosen to be one of the hijackers but couldn't get a U.S. visa to enter the country.
The judge presiding over the case, Army Col. James Pohl, ruled Monday over prosecutors' objections that the defendants have the right to be absent from this week's hearing. But Pohl didn't rule out requiring they attend future hearings and said they must attend their trial before a jury of military officers.
The chief prosecutor, Army Brig. Gen. Mark Martins, had argued that the rules for the special wartime tribunals known as military commissions require defendants to attend all court sessions.
Prosecutors also said in court papers that their presence was required to ensure that the proceedings are viewed as legitimate.
But lawyers for the men said the threat of forcible removal from their cells would be psychologically damaging for men who had been brutalized while held by the CIA in secret overseas prisons before being taken to Guantanamo in September 2006.
The judge did agree on Tuesday to give the defendants more leeway in choosing what they wear to court.
Mohammed and bin Attash had wanted to wear camouflage clothing in the courtroom at their May arraignment, apparently to portray themselves as soldiers, but the prison commander refused to allow it. The judge ruled they could wear some camouflage items as long as they were not U.S. military uniforms.
Defense lawyers have said that restrictions on their clothing had been one of the factors that led to their protest at their May arraignment, when the men ignored the judge's questions and wouldn't use the court's translation system. This week, the men have all appeared in traditional loose fitting traditional tunics, vests and hats that they chose to wear.
The judge also began hearing arguments Tuesday on a protective order, a set of rules for handling classified evidence that the defense and other critics say are overly broad.
Protective orders are standard in civilian and military trials, and prosecutors say the one proposed for the Sept. 11 trial is necessary to prevent the release of classified secrets.
But defense lawyers say the rule would make it harder for them to introduce the men's own accounts of the conditions of their captivity during the several years they each spent in CIA-run overseas prisons, where they were subjected to what the government calls "enhanced interrogation techniques" that critics equate to torture.
Mohammed and his four co-defendants face charges that include terrorism, conspiracy and 2,976 counts of murder in violation of the law of war, one count for each known victim of the Sept. 11 attacks at the time the charges were filed.