He added that Colonel Kane testified during the closed session that he was obeying the order in the Sept. 11 case.

Seventeen sailors were killed in the bombing of the U.S. Navy destroyer off Yemen on Oct. 12, 2000.

The shackling question is the first torture-related issue to confront the new Cole case judge, Colonel Fitzgerald. Last year, the previous judge threw out confessions Mr. Nashiri made at Guantánamo in 2007 as tainted by the prisoner’s brutal treatment in the agency’s overseas prison network. He was held at C.I.A. black sites from 2002 from 2006.

Mr. Nashiri was waterboarded by psychologists working as contractors for the C.I.A., held naked and shackled in painful “stress positions,” and subjected to threats and violence, including rectal abuse, by agency staff members. A court-ordered military medical assessment found that, as a result of his abuse, he suffers from complex post-traumatic stress disorder, depression and other conditions.

Commander Piette, who has represented Mr. Nashiri longer than any other member of his current defense team, said the resumption of shackling had harmed the prisoner’s ability to communicate with his lawyers because of a “cognitive change” triggered by his PTSD. To effectively represent him, Commander Piette said, Mr. Nashiri “has to trust his American lawyers, American lawyers dressed like me.”

While still murky, the problems at the prison first surfaced earlier this year when all four defendants in the Sept. 11 case, including Khalid Shaikh Mohammed, who is accused of being the mastermind of the attacks, chose not to come to weeks of pretrial hearings. Although they have the right to voluntarily waive their attendance before the trial actually begins, they were essentially engaging in a boycott.

In court last month, Denny LeBoeuf, a lawyer for Mr. Mohammed, protested to the judge, Col. Matthew N. McCall, that the prisoners had experienced “a level of upset and uproar from conditions at the camp and the transportation and meeting problems that is unprecedented in my experience.” She has been on the case since 2008.