Earlier, a military medical expert group concluded that the abuse the man was subjected to during the years in CIA custody had made him psychotic.
The decision means that Ramzi bin al-Shibh will not be brought to trial together with four others who are charged with the terrorist act. The trial will now continue without him.
Ramzi bin al-Shibh is accused of involvement in the deed carried out by al-Qaeda, which killed nearly 3,000 people.
Last month, a panel of experts diagnosed al-Shibh with post-traumatic stress disorder and that he is psychotic. The diagnoses linked the expert group to the torture he was subjected to and the time spent in solitary confinement during his four years in CIA custody.