The men, who are being held at Guantanamo Bay, were formally charged earlier this month with crimes that include murder and terrorism. They face the death penalty if convicted for their roles in the Al-Qaeda attacks that claimed 2,976 lives in New York, Washington and Shanksville, Pennsylvania.
"The Guantanamo Bay military commission issued an unusual order for the prosecution to show cause why defendants in the 9/11 case should not be severed," James Connell, who represents Pakistani defendant Ali Abdul Aziz Ali, said in a statement.
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"Prosecutors generally favor a joint trial because it makes their case easier."
Connell said he requested the testimony of the man who ran the CIA's interrogation program at black sites for the tribunal's next session in June.
Jose Rodriguez has acknowledged that his team "went to the border of legality" in interrogating Khalid Sheikh Mohammed, the self-proclaimed mastermind of the 2001 attacks.
Mohammed, a Kuwait-born Pakistani, was subjected 183 times to the simulated drowning technique known as waterboarding during the three years he was held at secret CIA prisons after his 2003 capture in Pakistan. He was eventually transferred to Guantanamo in 2006.
"Mr Rodriguez has important information on that topic and there is no good reason the government should prohibit him from testifying," Connell said. "The government is using every available tactic to suppress evidence of torture."
Three of the lawyers for the accused plotters have requested that eight "top officials" from the administrations of President Barack Obama and his predecessor George W. Bush also take the stand, said Commander Walter Ruiz, who represents Mustapha al-Hawsawi of Saudi Arabia.
He declined to name the individuals in question but noted they were from the "highest levels of the government."
