Defense lawyers for the alleged 9/11 plotters said for the first time Sunday that the government destroyed a secret CIA prison with secret permission of the trial judge, and they learned of it only after the fact.

Defense attorneys have been complaining about a mysterious destruction of evidence episode in a cloaked manner since May. Prosecutors have said they did nothing wrong but declined to explain with any specificity. After a closed session Friday, during which the judge apparently agreed some details were no longer classified, the defense lawyers laid out what they knew in a Sunday roundtable.

It did not appear that the “torture chamber,” as defense attorney Cheryl Bormann called it, was razed, lawyers said. Rather, their reading of case documents, some undergoing declassification, was that U.S. agents undertook a “decommissioning” of a secret, former overseas CIA “black site” still controlled by the United States. They got permission, for example, to removed “fixtures” — something defense attorney Suzanne Lachelier described as sounding like “contraptions or devices.”

Instead of seeing the U.S.-controlled former prison to “exercise our own professional judgment as to what to document about the black sites,” said defense attorney Jay Connell, the prosecution got permission from the judge to offer them a substitution: Top Secret photographs and diagrams of one stop in the CIA’s secret overseas network.

These were the places where from 2002 to 2006 CIA agents kept their captives naked, or in diapers, waterboarded some, rectally abused others, used cramped confinement boxes and hot and cold temperatures to break the men in their pursuit of al-Qaida secrets — techniques that the Senate Torture Report mostly described as ineffective. Guantánamo had two of the black sites.

None of the lawyers were privy to the name of the nation that hosted the site that was decommissioned. Part of why the prosecution was protecting it, they said, was to preserve foreign relations.

Now five former CIA captives led by alleged mastermind Khalid Sheik Mohammed are here for a military tribunal alleging they directed, trained or provided logistical support to the hijackers who killed 2,976 people on Sept. 11, 2001. Mohammed’s attorney, David Nevin, has argued that the site was of equal importance to all five accused, suggesting all five were confined there at one time or another.

Saturday, the chief prosecutor, Army Brig. Gen. Mark Martins would not speak to the specific issue of black site destruction. But he defended the process of substitution as created by Congress, first in the Classified Information Protection Act and now in the Military Commissions Act, “so that our court processes don’t squander national security and secrets.”

“We’re not going to let an individual criminal defendant ... mortgage the whole future of the country in one case, because they’ve got something that could force government officials to try to figure out how to accommodate it,” the general said. “We’re not allowed to compromise national security just to get to a result in a case. That’s what Congress is trying to prevent.”

Defense lawyers also for the first time solved a mystery that had surrounded the Pentagon’s two death-penalty prosecutions that seek to execute six former CIA prisoners: Two sets of top secret filings — known to the public as “the no-name motions” — sought permission to destroy the black site whose location was so secret the defense attorneys couldn’t even know it.

They’ve been under seal for years, as AE92 in the USS Cole case and as AE52 in the 9/11 case.

Defense attorneys in classified filings and hearings opposed the destruction, they thought, to a standstill on the issue in June 2014. Instead, they said Sunday, prosecutors notified them this February of the site’s decommissioning. Defense attorneys said the 9/11 prosecutors held at least one secret session with the judge, Army Col. James L. Pohl.

Defense lawyer said they did not know if Pohl personally inspected the prison before it was decommissioned.

Prosecutor Martins on Saturday refused to speak to specifics of the emerging battle over the destruction of evidence that has prompted four of the five defense teams to ask Pohl to disqualify himself and the prosecution team from the case. But he showed reporters the portion of the Manual for Military Commissions that permits the prosecution to meet secretly with the judge to create such substitutions.

The one team that does not seek Pohl’s recusal has proposed a different remedy. The lead lawyer for Mustafa al Hawsawi, a Saudi, said Sunday he wants Pohl to eliminate the possibility of the death penalty for his client.

Hawsawi’s attorney, Walter Ruiz, said Sunday his 47-year-old client “continues to bleed daily” from rectal abuse inflicted during CIA custody. Defense medical experts say Hawsawi’s injuries require surgery but are treated with ointment at Guantánamo’s Camp 7.