Judge Army Colonel James Pohl issued the ruling after a closed session in which Walid bin Attash, one of five defendants in the slow-moving death penalty case, had argued why defense lawyer Cheryl Bormann should be replaced.
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"You have not shown good cause and as a result I will not terminate Bormann’s relationship with you," Pohl said during a pre-trial hearing at the US military base at Guantanamo Bay, Cuba.
The issue of bin Attash's legal representation has stalled the hearings involving him and the others charged in the September 11, 2001, attacks on the United States. Hearings resumed last week after an 18-month delay caused by an FBI investigation of defense attorneys accused of a security breach.
Bin Attash had said he did not trust Bormann, a Chicago lawyer who has represented him since 2011. He also has indicated he is frustrated that Bormann and his military attorney, Air Force Major Michael Schwartz, have not been able to resolve complaints about conditions at the US base where he is being held.
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Bin Attash is charged with hijacking, terrorism, war crimes and conspiring with militants who slammed hijacked airliners into New York's World Trade Center, the Pentagon and a Pennsylvania field. He also allegedly ran an al Qaeda training camp in Afghanistan.
Pohl also rejected a defense request for an investigation into Defense Secretary Ashton Carter's criticism of an order Pohl issued in January.
Pohl's order barred female guards from touching or transporting prisoners. The suspects have complained that being touched by a woman other than their wives violated Muslim tradition.
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Carter called the ruling "outrageous" in a Senate Armed Services Committee hearing on Tuesday. Marine Major Derek Poteet, a lawyer for alleged September 11 mastermind Khalid Sheikh Mohammed, said the comments constituted unlawful influence over the court and called for an investigation.
Pohl said criticism of him was nothing new and questions about unlawful influence could be handled through pre-trial procedures.
The hearing was carried over closed-circuit television to a media center at Fort Meade, outside Washington.
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