NEW YORK >> The military judge in the USS Cole bombing case on Friday threw out confessions the Saudi defendant had made to federal agents at Guantánamo Bay after years of secret imprisonment by the CIA, declaring the statements the product of torture.

The decision deprives prosecutors of a key piece of evidence against Abd al Rahim al-Nashiri, 58, in the longest-running death-penalty case at Guantánamo Bay. He is accused of orchestrating al-Qaida’s suicide bombing of the warship on Oct. 12, 2000, in Yemen’s Aden Harbor that killed 17 U.S. sailors.

“Exclusion of such evidence is not without societal costs,” the judge, Col. Lanny J. Acosta Jr., wrote in a 50-page decision. “However, permitting the admission of evidence obtained by or derived from torture by the same government that seeks to prosecute and execute the accused may have even greater societal costs.”

The question of whether the confessions were admissible had been seen as a crucial test of a more than decadelong joint effort by the Justice and Defense Departments to prosecute accused architects of al-Qaida attacks at the special Guantánamo court, which was designed to grapple with the impact of earlier, violent CIA interrogations while pursuing justice through death-penalty trials.

Similar efforts to suppress confessions as tainted by torture are being made in the case against Khalid Sheikh Mohammed and four other prisoners who are accused of conspiring in the terrorist attacks of Sept. 11, 2001. Nashiri, like Mohammed, was waterboarded and subjected to other forms of torture in 2002 by CIA interrogators, including contract psychologists, through a program of “enhanced interrogation.”

Testimony showed that the psychologists took part in a yearslong program that, even after the violent interrogation techniques ended, used isolation, sleep deprivation, punishment for defiance and implied threats of more violence to keep the prisoners cooperative and speaking to interrogators.

Prosecutors considered Nashiri’s confessions to federal and Navy criminal investigative agents at Guantánamo in early 2007, four months after his transfer from a CIA prison, to be among the best evidence against him.

But prosecutors also sought, and received permission from the judge, to use a transcript from other questioning at Nashiri’s eventual trial.

In March 2007, he went before a military panel examining his status as an enemy combatant and was allowed to address allegations involving his role in al-Qaida plots. He told military officers that he had confessed after being tortured by the CIA, but then recanted.

At the administrative hearing, Nashiri denied being a member of al-Qaida or involvement in the plots but admitted to knowing Osama bin Laden and receiving funds from him for an unrealized shipping business project in the Persian Gulf.

Human rights and international law experts had been eagerly awaiting the decision as a test of a U.S. government theory that federal agents could obtain a lawful confession, untainted by previous abuse, if so-called clean teams questioned the defendants without threats or violence and repeatedly told former CIA prisoners that their participation was voluntary.

But testimony in the pretrial hearings showed that after his capture in 2002, Nashiri was subjected to both authorized and unauthorized physical and emotional torture in an odyssey through the CIA secret prison network — from Thailand to Poland to Afghanistan and then Guantánamo Bay — that including waterboarding, confinement inside a cramped box, rectal abuse and being tormented with a revving drill beside his hooded head to coerce him to answer interrogators’ questions about future and suspected al-Qaida plots.

By the time he was questioned by federal agents in January 2007, lawyers and experts argued, the prisoner was trained to respond to his interrogators’ questions.

Acosta, who retires from the Army next month, agreed.

Nashiri had no reason to believe “that his circumstances had substantially changed when he was marched in to be interviewed by the newest round of U.S. personnel in late January 2007,” Acosta said.

“If there was ever a case where the circumstances of an accused’s prior statements impacted his ability to make a later voluntary statement, this is such a case. Even if the 2007 statements were not obtained by torture or cruel, inhuman, and degrading treatment, they were derived from it.”

Rear Adm. Aaron C. Rugh, the chief prosecutor for military commissions, did not respond to a question about whether his team would appeal the ruling. With a new judge expected later this year, prosecutors could seek reconsideration at the Guantánamo court or raise the issue with a Pentagon appeals panel, the Court of Military Commissions Review.

Separately, the panel is considering a challenge to Acosta’s status as the judge in the USS Cole case. Defense lawyers had asked him to step down earlier this year when he disclosed that he was applying for a post-retirement, civilian job as clerk of the Air Force Judiciary. Acosta refused, saying he had disclosed his application the day after he applied for the job, and so there was no hidden bias in favor of the government.

Katie Carmon, one of Nashiri’s lawyers, said there were no immediate plans to withdraw their challenge and called Acosta’s decision suppressing the 2007 interrogations both “morally and legally correct.”

“The government that tortured al-Nashiri has never been held accountable,” she said. “But today’s ruling is a small step forward as the government loses a critical part of its prosecution.”

This article originally appeared in The New York Times.

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