Mr. Nashiri’s lawyers were exploring a potential defense theory that the United States had already killed plotters of the Cole attack who were more senior and more culpable. The prosecutors asked the judge to end that line of inquiry, pointing to a classified cable that said Mr. Nashiri had told C.I.A. agents as he was being interrogated at a secret prison in Afghanistan that Mr. Fadhli had not been involved.
Defense lawyers said the law prohibited the use of the statement — or any statement by a defendant that was derived from torture or any other cruel, inhuman or degrading treatment — throughout the entire proceedings. Prosecutors argued there was an exception for the period when a judge decided pretrial matters before a military jury was chosen to hear a case.
The military judge, Col. Lanny J. Acosta Jr., agreed with the prosecutors in a ruling dated May 18, 2021, that still stands.
Defense lawyers in the case said Tuesday that they were troubled by the language in the Justice Department filing that left open the possibility of an exception for a future administration, particularly given the longevity of the prosecution. It was originally conceived by the Bush administration and pursued by the Obama administration. It has been subject to long delays caused by both prosecution and defense appeals of rulings by the Guantánamo judges.
“It is a cause for concern,” said Michel Paradis, an appellate lawyer for Mr. Nashiri, who works for the Department of Defense. “The Trump administration took a very different view of torture than the Biden administration does. And this pleading leaves open the discretion to change their position.”
Also of concern, he said, was the government’s disclosure in the filing on Monday night that a war court prosecutor, in a review of 100,000 pages of secret filings, discovered another instance when prosecutors invoked something Mr. Nashiri told the C.I.A. at one of their black sites. It was in a 2014 filing.
Defense lawyers were unaware of the use of the statement from the black sites because, at the national security court, prosecutors can give information to the judge unilaterally in a process that enables them to protect, redact or rephrase classified information. The defense lawyers were weighing on Tuesday whether to seek a more vigorous, independent examination of the 100,000 pages.