WASHINGTON — War court prosecutors of the five men accused of plotting the Sept. 11 attacks used classification rules to choke off public testimony about whether the C.I.A. or the United States military was in charge of Guantánamo Bay's most secret prison after it opened in 2006, a military judge ruled this week.
The answer to that question could influence whether F.B.I. interrogations of Khalid Shaikh Mohammed and four other men accused of conspiring in the attacks that killed 2,976 people on Sept. 11, 2001, could be used at their trial, which is scheduled to start in January 2021.
The judge, Col. W. Shane Cohen of the Air Force, ordered the prosecutors to find a way for defense lawyers to challenge in open court an opinion offered by the first commander of Camp 7, a classified prison — that the United States military ran the facility once Mr. Mohammed and the others were transferred to Guantánamo in 2006 from years in C.I.A. black sites.
Otherwise, the judge said, he will exclude the opinion from evidence he is taking in long-running pretrial hearings that are now addressing whether the F.B.I. interrogations in 2007 of the five men at Guantánamo will be admissible at the trial.
The former Army lieutenant colonel testified on Nov. 1 that he ran the prison from 2006 to 2008 and disagreed with a finding in the Senate Intelligence Committee study known as the Torture Report that the C.I.A. had "operational control" of the high-value prisoners in Camp 7 at the time.
A prosecutor, Robert Swann, then declared that any exploration of that opinion would have to take place in a closed, national security session — denying the public the opportunity to know how the commander could come to a different conclusion than the Senate.
The issue illustrates the current state of the pretrial hearings in the Sept. 11 case, which began in 2012. Increasingly, prosecutors consult the intelligence agencies on what the public, and defendants, are allowed to hear and then divide testimony between open and closed hearings.
The next hearing, to begin on Jan. 21 and last two weeks, is expected to take testimony from one or two of the contract psychologists who proposed and enforced the C.I.A.'s so-called enhanced interrogation program of waterboarding, sleep deprivation and other methods that have since been outlawed. The program was used to break prisoners the agency held incommunicado from 2002 to 2006. It is still unclear how much of the testimony by the two men — James E. Mitchell and John Bruce Jessen — the public will be allowed to hear, and how much the prosecutors will declare classified.
The testimony by the psychologists as well as the former prison commander is to help the judge decide whether the defendants voluntarily described their alleged roles in the attacks when they were questioned by F.B.I. agents in early 2007 at Guantánamo, months after their transfer from years in C.I.A. custody. Defense lawyers argue that any confessions the men made were tainted by torture, and they seek to call dozens more witnesses in the pretrial phase.
The former Camp 7 commander testified anonymously that he served for 19 months as the first commander of Guantánamo's Task Force Platinum and was at the base airstrip in southeast Cuba when the C.I.A. delivered Mr. Mohammed and 13 other "high-value detainees" to Guantánamo.
Even though the men were guarded by a secret, nonmilitary force disguised as American troops, the former commander said those forces "responded to my orders consistently." Because of that, he disagreed with a Senate study that found that the defendants of the Sept. 11 attack and other recent arrivals "remained under the operational control of the C.I.A." for an undisclosed amount of time.
The finding was made public in 2014 with the release of a mostly declassified summary of the full 6,700-page study on the C.IA.'s detention and interrogation program. But any details on the C.I.A.'s role then, and now, at Camp 7 are considered classified.
Defense lawyers protested the restriction on questioning the camp commander. Gary D. Sowards, Mr. Mohammed's lawyer, said prosecutors were using "classification and security privileges to control the narrative." He called it "an ongoing theme" that distorts the public record of the trial "by design or by effect."
Colonel Cohen wrote in the decision dated Monday that, before asking the question, prosecutors issued classification guidance that required defense lawyers to challenge that opinion "in a hearing closed to the public." He said that "procedure" in that instance was "prejudicial to the accused because it exposes the public to only the government's side of the case."
He also said it "undermines public confidence" in the proceedings of the military commission, the military court that blends some federal court rules in a tribunal system that the Bush administration created in response to the Sept. 11 attacks.
Because the government, represented by both Defense and Justice Departments prosecutors, controls what is classified at the trial, the judge gave the prosecution until Jan. 13 to draft "an unclassified summary of the classified facts sufficient to allow the defense to cross-examine the first Camp VII commander in open court regarding his opinion."