The critical question of whether the prisoner’s 2007 interrogations could be used at his capital trial has shadowed the case for years.
A military judge on Friday threw out the confession that a man accused of conspiring in the Sept. 11 attacks made to federal agents in 2007 at Guantánamo Bay, ruling the statements were the product of a campaign of torture and isolation carried out by the C.I.A.
The ruling by Col. Matthew N. McCall was the latest setback to prosecutors in their long-running quest to bring the death-penalty case to trial, despite the years the five defendants had spent in secret C.I.A. prisons.
Ammar al-Baluchi, 47, was so thoroughly psychologically conditioned through abuse and threats during his time at the agency’s overseas prisons, or black sites, from 2003 to 2006 that he involuntarily incriminated himself in 2007, the judge wrote in a 111-page decision.
Mr. Baluchi, who is charged in the case by the name Ali Abdul Aziz Ali, is accused of sending money and providing other support to some of the hijackers who carried out the attack that killed nearly 3,000 people on Sept. 11, 2001.
He is the nephew of Khalid Shaikh Mohammed, the man accused of masterminding the attack. Mr. Mohammed and two other defendants in the case reached plea agreements with prosecutors that are now being contested in federal court. A fifth defendant was found mentally unfit to stand trial, a condition his lawyer blames on his torture at the hands of the C.I.A.
Testimony derived from C.I.A. documents showed that Mr. Baluchi was routinely kept naked and beaten during his first days of agency custody in a program of “enhanced interrogation,” which was designed by two psychologists on contract to the C.I.A.