The order came during the military tribunal for Abd al Rahim al-Nashiri, accused mastermind of the 2000 attack on the USS Cole in Yemen, which killed 17 American sailors and wounded 42 others.
Nashiri was held at several secret CIA prisons before being shipped to Guantánamo Bay, where he has been detained since 2006.
His lawyers contend that he was tortured at the clandestine facilities, including being subjected to waterboarding and threats involving a gun and a power drill while CIA officials sought information from him about future terrorist plots.
The defense team wants the CIA to disclose its records of what took place, in order to challenge certain evidence against Nashiri in the hope it will keep him from being executed if he is convicted.