Mohammed, who has repeatedly acknowledged his guilt on charges that could lead to his execution, later told the court, "We don't care about the capital punishment...we are doing jihad for the cause of God."
The hearing could be the last to be held at the Guantanamo military court, as Barack Obama, the US president-elect, has said he wants to shut down the detention centre amid continued pressure from human rights groups over the treatment of detainees.
The CIA acknowledged earlier this year that Mohammed had been interrogated using the controversial "waterboarding" technique which simulates drowning.
If the Guantanamo Bay were to be closed, the legal status of the tribunals and the detainees themselves would be unclear.
The judges were considering whether the Pentagon must charge the men all over again after it withdrew and refiled charges in about 20 cases.
The Pentagon had described the refiling as a procedural step required to appoint new military jury panel members.
The judges agreed that the tribunals could continue without new charges.
In December, the five defendants said they wished to submit guilty pleas to the terror charges against them, pending mental competency evaluations.
If the pleas go forward, they could be sentenced to death.
Of the 245 inmates still being held at Guantanamo Bay detention centre, only about 20 have been charged, including the five men accused of conspiring to plot the 9/11 attacks.
Mohammed, Binalshibh and three others, Mustafa Ahmed al-Hawsawi, Walid bin Attash and Mohammed's nephew, Ali Abdul Aziz Ali, face 2,973 counts of murder, one for each person killed when fighters crashed hijacked airliners into the World Trade Center, the Pentagon and a Pennsylvania field in 2001.