Three of the five alleged Sept. 11 conspirators, including mastermind Khalid Shaikh Mohammed, refused to attend a pretrial hearing Tuesday over evidence in their trial at Guantánamo.

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FORT MEADE, Md. — Three of the five alleged Sept. 11 conspirators, including mastermind Khalid Shaikh Mohammed, refused to attend a pretrial hearing Tuesday where lawyers argued over one of the significant overlying issues in the case — whether potential evidence of torture and other classified material will be discussed publicly in their trial at the U.S. Naval Base on Guantánamo Bay, Cuba.

The government wants a protective order prohibiting the release of material from the defendants’ custody at “CIA black sites” before being moved to Guantánamo Bay in 2006. Defense lawyers complain that in addition to hampering them at trial, the restrictions block them from even discussing those events with their clients, including Mohammed, who was waterboarded 183 times.

The issue is crucial to both sides. Prosecutors do not want trial jurors hearing about torture or other “enhanced interrogation techniques,” and argue it would be a “sideshow” distracting from whether the defendants are guilty of conspiracy and terrorism in the 2001 attacks that killed nearly 3,000.

But defense lawyers said that restriction would severely handicap them in strategizing on how best to defend the clients in the capital murder trial, tentatively scheduled to begin next May.

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“They’re holding our clients in isolation,” said an exasperated Navy Lt. Cmdr. Kevin Bogucki, an attorney for Ramzi Binalshibh, who allegedly managed the cell for the plane attacks in New York, Washington, D.C., and Pennsylvania.

Cheryl Bormann, a lawyer for Walid bin Attash, an alleged al-Qaida training camp steward, was equally frustrated with limited access to her client in the heavily guarded prison.

“He can’t call me to say he’s sick,” she said. “We can’t write to our clients. Now on top of it I have additional rules and this protective order is completely unnecessary. It would be creating more difficulties.”

But Joanna Baltes, a Department of Justice attorney and deputy trial counsel for the prosecution, said the government must ensure against leaks of classified national-security information.

“We want to prosecute this case and go forward and not be constantly concerned about classified information being harmed,” Baltes told the judge.

“The government is not seeking to impose any restrictions on the accused themselves,” she added. “The restrictions and the obligations are strictly on the attorneys who hold security clearances in this case.”

The judge, Army Col. James Pohl, also heard from attorneys for news organizations and the American Civil Liberties Union who urged for greater public access to the case.

Pohl did not rule on the matter.

On Monday, Pohl ruled for the defense by allowing defendants to voluntarily choose not to attend each day’s proceedings, an offer Mohammed and two others accepted Tuesday.

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