But Moussaoui's lawyers have filed an appeal, contending that government officials withheld evidence from his defense, and that the CIA had submitted inaccurate declarations to the U.S. District Court that no recordings of detainee interrogations existed.
In late 2007, court documents filed in the appeal revealed that the CIA had obtained three recordings "under unique circumstances involving separate national security matters unrelated to the Moussaoui Prosecution."
Government attorneys submitted transcripts to the court, but said it was unclear from the court documents whether the tapes still existed.
In his statement, CIA spokesman Gimigliano said that the tapes mentioned in the 2007 filings in the Moussaoui case are not the same as the tapes referred to in the ACLU suit.
"Those three tapes still exist. It's a separate issue," he said.
As for the most recent admission from the CIA concerning the 92 destroyed tapes, Moussaoui's legal team had learned of their existence as much as a month ago.
In transcripts declassified and released late last Friday, Moussaoui's lawyers say that the revelation that there "could be a whole bunch of other tapes" should cause the case to be sent back to the court that originally handled the case.
The U.S. Court of Appeals for the Fourth Circuit is currently considering that request.
Last summer, then-Attorney General Michael Mukasey notified lawmakers that he would not appoint a special prosecutor to investigate the actions of CIA interrogators.
Noting that Justice Department lawyers had authorized the controversial techniques, Mukasey said in a letter to House Judiciary Chairman Rep. John Conyers, D-Mich., that "it would be unwise and unjust to expose to possible criminal penalties those who relied in good faith on those prior Justice Department opinions."
ABC News' Ariane de Vogue contributed to this report.