Defense lawyers were not permitted to remove their notes from the room or to share details of classified information with their clients.
The boxed materials included electronic discs, as well as about 80 volumes of translated summaries of conversations, Jacks said in court papers.
The mistakenly released portions of the evidence included some of the electronic communications and Foreign Intelligence Surveillance Act material, including orders by the top-secret court.
During a review of what defense lawyers characterized as a mountain of documents "piled indiscriminately in unmarked boxes," FBI agents discovered the error.
"Many documents were not stapled and pages were out of order," defense lawyers told the judge in a motion.
"The government provided no index. In short, it is clear from the condition of the documents and manner of production that the government took no steps to track and record the documents produced and did not perform any quality control."
Jacks immediately sought to retrieve the documents, according to court records.
He contacted a court security officer and asked for access to the sealed room. The security official refused and said the prosecutor would need defense counsel's approval to enter.
At that point, Jacks contacted a defense lawyer and asked for access. Again, it was denied.
Jacks finally went to the secure room while defense lawyers were there and "demanded to know what counsel were doing," according to a defense motion.
Jacks declined to comment Wednesday, but in court papers he defended his efforts to recover the documents.
"The government's paramount interest in seeking the return of the information ... is to protect the integrity of highly classified and national security information to which no defense counsel in the instant case is entitled," he said in a Sept. 16 letter to the court.
U.S. District Judge A. Joe Fish ruled the documents off-limits to both sides and took custody of them. They remain in his chambers.
Citing the classified nature of the material, defense lawyers declined to comment.