"The defense is asking the Obama administration to suspend the military commission and transfer these men [the defendants] to federal courts," Al Jazeera's Monica Villamizar reported from Guantanamo.
Eric Holder, the incoming attorney general, said during his confirmation hearing that Obama was already preparing to make his first moves to close the detention centre.
But relatives of those killed in the September 11 attacks, who were present at Monday's hearings, called for Guantanamo to remain open and for the military commissions to try the "suspected terrorists".
"There is a lot of anxiety, especially on behalf of the relatives of the 9/11 victims who have said that they want justice for those blamed for the attacks," Villamizar said.
"The chief prosecutor has said that he will certainly be arguing that the death penalty is appropriate."
Khalid Sheikh Mohammed appeared before the tribunal with co-defendants Ali Abd al-Aziz Ali, Walid bin Attash, Mustapha al-Hawsawi and Ramzi Binalshibh.
He said he had been tortured and that this was "terrorism, not court", while Binalshibh declared he was "proud of September 11".
The judge presiding the court acknowledged the uncertainty around the future of the proceedings, referring a legal question to "later sessions, if later sessions are scheduled".
Closing Guantanamo could take several months, as US officials will have to transfer a part of the 245 prisoners currently held to other countries and try the remaining suspects in US courts.
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 September 11 attacks.