GUANTANAMO BAY NAVY BASE, Cuba -- In unprecedented war court testimony, the prison camps’ commander on Tuesday defended a three-tier system of classifying lawyers’ mail to alleged terrorists that sparked a defense lawyer’s boycott and is threatening to stall future war crimes trials.

It was the first time the camps’ top commander testified at a Guantánamo military commission. Rear Adm. David B. Woods said he had a team of Defense Department contractors examining confidential, privileged attorney-client mail for “safety, force protection and good order.”

At issue is whether the prison camps staff is complying with the chief military commissions judge’s November order to look at, but not read, defense lawyers documents for alleged USS Cole bomber Abd al Rahim al Nashiri that are marked “privileged.”

Woods testified that the contractors are assigned to discern whether lawyers mail is indeed privileged or more generic legal mail. The contractors include former government lawyers, law enforcement officials, linguists and Woods wants them looking at documents for things like diagrams that might threaten security inside the prison camps that hold some 171 foreign captives.

Only Nashiri is currently charged with a war crime, and Pentagon prosecutors are seeking his military execution. The 47-year-old former millionaire from Mecca allegedly orchestrated the October 2000 bombing of the destroyer off Yemen that killed 17 U.S. sailors.

Army Col. James Pohl, the war court judge, summoned Admiral Woods to Camp Justice on less than 90 minutes notice. Even though the admiral outranks him, war court legal officials advised reporters, Woods had to comply with the order.

The admiral donned his Navy blues rather than the desert combat uniform he usually wears to work here. And he was late, drawing an admonition to case prosecutors to get their witnesses to court on time. “I don’t care what their rank is,” the judge said.

Pohl did not rule on the prison camps’ mail review system.

He’ll hear more testimony and arguments on Wednesday.

But the conflict has threatened the future of the war crimes trials.

If the contractors dispute a war court defense lawyer’s decision to stamp a document privileged, under a new policy, Woods as prison camps commander will decide the issue. Except in the Nashiri case, when the admiral will ask the war court judge to do it.

Woods notified commission lawyers of the new policy late last year, sparking a rebellion by an office that before had their “privilege” stamps honored. The chief Defense Counsel, Marine Col. Jeffrey Colwell, advised all military commissions lawyers to stop sending confidential mail to their clients, including the lawyers getting ready for death penalty case against five alleged plotters of the 9/11 attacks.

Defense lawyers argue that a system that answers to the prison camps commander, effectively the warden, violates their ethical obligations as officers of the court. It was unclear Tuesday what contracting firm precisely had the job of sifting through the mail, nor the value of the contract.

Woods, on the job since August, identified the firm in court as the United States Defense Intelligence, USDI.

But Pentagon spokesmen at Guantanamo said that was the acronym for the Defense Department’s Undersecretary of Defense Intelligence, a government entity, not the private contractor entrusted with reviewing privileged mail. They could not immediately name the contractor, nor say whether it's funded through the prison camps’ $800,000-a-year per captive operating budget.

The Chief War Crimes prosecutor, Army Brig. Gen. Mark Martins, said that whatever the contract they are obliged to behave responsibly.

The Chief Defense Counsel, Colwell, said Tuesday’s testimony did not change his advice to Pentagon defenders to stop sending mail to Guantánamo captives that they consider privileged.

“The orders require our attorneys to submit privileged information to an undefined privilege team that we learned today, no one really knows who they work for,” Colwell added. “And they certainly don’t work for the judge.”

In a separate decision, the war court judge rejected a request from Nashiri’s attorneys to allow the former CIA captive to be unshackled during meetings with his lawyers.

Defense lawyer Rick Kammen said Nashiri was traumatized by his treatment in CIA custody — waterboarding, being threatened with a gun and a power drill, all while shackled at the ankles — in the years before he was brought to Guantánamo in 2006.

The judge said the lawyers hadn’t shown evidence that the man was impaired. Meantime, prison camp guards get to decide how to appropriately secure the alleged terrorist during attorney-client meetings.

Nashiri listened to the proceedings alongside his lawyers in the white prison camp uniform of a cooperative captive. He was unshackled and on occasion appeared to fidget. Unlike at his first court hearing in November, he glanced back but didn’t wave at the viewing gallery.