WASHINGTON (Reuters) - The U.S. military judge overseeing the trial of the accused mastermind of the Sept. 11 attacks should step down and the case should be scrapped because he effectively conspired with prosecutors to destroy evidence, defense lawyers said in a court filing.

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The motion said Judge James Pohl, an Army colonel, and prosecutors had tainted the case against Pakistan-born Khalid Sheikh Mohammed by keeping defense lawyers from learning that the evidence had been destroyed.

The motion was filed on May 10 and recently cleared for release. It raises a potential hurdle in the slow-moving capital case against Mohammed and four others charged in the hijacked airliner attacks of Sept. 11, 2001, in which 3,000 people died.

Pohl, along with prosecutors, “manipulated secret proceedings and the use of secret orders to mislead the defense and unfairly deprive Mr. Mohammed” of ways to keep the evidence from being destroyed, the motion said.

Commissions spokeswoman Lieutenant Colonel Valerie Henderson referred questions to the prosecutor’s response, which is expected to be made public in a few days.

Pohl presided over a pretrial hearing on Tuesday in the case at the U.S. Navy prison at Guantanamo Bay, Cuba.

The filing alleges that Pohl authorized prosecutors to destroy evidence six months after he agreed to a defense request that it be preserved.

Defense lawyers were kept in the dark about the authorization and the contact between Pohl and prosecutors, it said.

Pohl’s order had included a provision that prosecutors give a redacted version of it to the defense. But he did not tell them to do so until 18 months after the order was issued, long after the evidence was destroyed, the filing said.

The motion does not detail what the evidence was, and classified annexes are sealed. A prosecution response filed last week has not been cleared for release.

The motion asks that Pohl recuse himself and that Army Brigadier General Mark Martins, the military commissions’ chief prosecutor, and the prosecution team be disqualified. It also asks that Mohammed’s trial be scrapped and/or the death penalty be dropped.

Martins had no immediate comment.

During Tuesday’s hearing, prosecutors asked Pohl to let 10 relatives of Sept. 11 victims testify in open court. Reuters monitored the proceedings from a media center at Fort Meade, Maryland, outside Washington.

The case is among a half dozen against Guantanamo inmates.