This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

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.