GUANTÁNAMO BAY, Cuba — Prosecutors in the case of a Qaeda suspect misrepresented to defense lawyers what happened to him in C.I.A. custody, a military judge has ruled, complicating efforts to bring the suspect to trial at Guantánamo Bay and raising new questions about how the military commission system is dealing with the legacy of the C.I.A.’s secret prisons.
The ruling came in the case of Abd al Rahim al Nashiri, a Saudi man who is accused of orchestrating the Oct. 12, 2000, bombing by Al Qaeda of the warship Cole off Yemen that killed 17 American sailors.
He was captured in 2002 in Dubai; subjected to waterboarding, sleep deprivation, a mock execution and other violence in the C.I.A. secret prison network; and then transferred in 2006 to Guantánamo for trial. In preparation for his trial, prosecutors had been providing his defense team with summaries or redacted versions of evidence related to his detention in the so-called C.I.A. black sites, with the ability to remove material based on national security concerns.
In a 23-page ruling dated Thursday, the judge, Col. Lanny J. Acosta Jr. of the Army, said that he reviewed a sample of evidence provided to defense lawyers and found “deletions that could fairly be characterized as self-serving and calculated to avoid embarrassment,” and “indicative of a minimalist view” of evidence defense lawyers were entitled to receive.
A best-case interpretation, he wrote, was that “standards have eased significantly” since prosecutors gave defense lawyers accounts of what the C.I.A. did to Mr. Nashiri at the black sites.
Colonel Acosta took over the death penalty case in February and has scheduled the first pretrial hearing for early December at Guantánamo.
In his ruling, Colonel Acosta also declined a request by prosecutors to reinstate 30,000 pages of court filings that a federal court vacated last year. The United States Court of Appeals for the District of Columbia Circuit threw out the filings when it found the previous judge, Col. Vance H. Spath of the Air Force, had a conflict of interest while he handled the case because he was secretly negotiating with the Justice Department for an immigration court judge job.
The system for handling classified evidence in the Cole prosecution is the same as the one being used in the other major case at Guantánamo: the trial of the accused plotters of the Sept. 11, 2001, attacks, which is scheduled to begin in January 2021. Colonel Acosta described the system for handling classified C.I.A. evidence as flawed and unfair to the defense.
“The government has failed to adequately assert the Classified Information privilege,” he said, and is relying on government invocations of national security that are both too broad and too old.
The process that has developed at the war court since Mr. Nashiri was charged allows prosecutors to decide which portions of classified evidence from the C.I.A. black sites the defense lawyers need to prepare for trial. The prosecutors consult with representatives of the intelligence community and then redact portions of reports from the C.I.A. black sites or write summaries to substitute for the actual evidence. They then provide the evidence to the trial judge to approve as an adequate substitution for defense lawyers.
“Many of the summaries are so significantly altered that they seem insufficient to meet the requirement that they place the defense in substantially the same position as would discovery of the underlying documents,” the judge wrote. “While limited redactions of certainly highly sensitive information may make sense, wholesale paraphrasing and obfuscation is not only extraordinarily onerous, it impacts reliability and usability.”
Colonel Acosta said that “tens of thousands of pages” have gone through that process in the Cole case and that prosecutors have so far failed to justify why “a handful” of defense lawyers on the Nashiri case cannot see the original evidence. Like the prosecutors, defense lawyers who practice in the national security trials at Guantánamo must have top-secret compartmentalized security clearances to work on the cases.
To evaluate the process, the judge said, he compared C.I.A. cables released through the Freedom of Information Act to versions of the same information provided to the defense in the case and found “the comparison undermines any contention the redactions are narrowly tailored to a legitimate need to protect national security.”
In one example provided to the judge, according to lawyers with knowledge of the filing, a cable from a C.I.A. black site in December 2002 that was made public this year described Mr. Nashiri as hooded and shackled up against a wall when an interrogator and linguist “strode, catlike, into the well-lit confines of the cell.”
The account of that same interrogation that prosecutors gave defense lawyers for Mr. Nashiri omitted the word “catlike.”
The National Security Archive at George Washington University obtained that document this year through a Freedom of Information Act filing that sought accounts from a secret prison that for a time was run by Gina Haspel before she became C.I.A. director.
The chief war crimes prosecutor, Brig. Gen. Mark S. Martins of the Army, and the other Cole case prosecutors have until Nov. 17 to decide whether to ask the judge to reconsider or to appeal to the military commission appellate panel.
Colonel Acosta issued the ruling as defense lawyers in the 9/11 case were at Guantánamo taking witness testimony. The defense lawyers are trying to get the judge to exclude F.B.I. accounts of what the accused terrorists told them in 2007 — after their transfer to Guantánamo from the black sites — as tainted by torture and F.B.I. collaboration with the C.I.A. over their interrogations in the black sites.
Defense lawyers in both cases say they need accurate, graphic descriptions of what the C.I.A. did to their captives in the secret prison network from 2002 to 2006. If the prisoners are convicted, they want to use the descriptions to persuade the military jury that the United States lost the moral authority to execute them.
This week, Colonel Acosta also ordered prosecutors in the Cole case to provide defense lawyers with information “regarding intrusions into attorney-client communications,” a decision that could further delay the timetable to a trial.
In the summer of 2018, Mr. Nashiri’s lawyers discovered an eavesdropping system in their client meeting room at the prison and were denied a request to investigate who, if anyone, was listening in on confidential conversations. The previous judge, Colonel Spath, refused to order release of that information or to let defense lawyers discuss it in public, prompting a walkout in October 2018 by Mr. Nashiri’s entire defense team.
“These allegations have already had a chilling effect, contributed to lengthy delays, and led to the withdrawal of three defense counsel,” Colonel Acosta wrote in that ruling. “The first step to ameliorating the issue is discovery.”