By Robert Windrem and Victor Limjoco

The 9/11 Commission suspected that critical information it used in its landmark report was the product of harsh interrogations of al-Qaida operatives - interrogations that many critics have labeled torture. Yet, commission staffers never questioned the agency about the interrogation techniques and in fact ordered a second round of interrogations specifically to ask additional questions of the same operatives, NBC News has learned.

Those conclusions are the result of an extensive NBC News analysis of the 9/11 Commission’s Final Report and interviews with Commission staffers and current and former U.S. intelligence officials.

The analysis shows that much of what was reported about the planning and execution of the terror attacks on New York and Washington was derived from the interrogations of high-ranking al-Qaida operatives. Each had been subjected to "enhanced interrogation techniques." Some were even subjected to waterboarding, the most controversial of the techniques, which simulates drowning.

The NBC News analysis shows that more than one quarter of all footnotes in the 9/11 Report refer to CIA interrogations of al-Qaida operatives who were subjected to the now-controversial interrogation techniques. In fact, information derived from the interrogations is central to the Report’s most critical chapters, those on the planning and execution of the attacks. The analysis also shows - and agency and commission staffers concur - there was a separate, second round of interrogations in early 2004, done specifically to answer new questions from the Commission.

9/11 Commission staffers say they "guessed" but did not know for certain that harsh techniques had been used, and they were concerned that the techniques had affected the operatives’ credibility. At least four of the operatives whose interrogation figured in the 9/11 Commission Report have claimed that they told interrogators critical information as a way to stop being "tortured." The claims came during their hearings last spring at the U.S. military facility in Guantanamo Bay, Cuba.

"We were not aware, but we guessed, that things like that were going on," Philip Zelikow, the 9/11 Commission executive director, told NBC News. "We were wary…we tried to find different sources to enhance our credibility."

Specifically, the NBC News analysis shows 441 of the more than 1,700 footnotes in the Commission’s Final Report refer to the CIA interrogations. Moreover, most of the information in Chapters 5, 6 and 7 of the Report came from the interrogations. Those chapters cover the initial planning for the attack, the assembling of terrorist cells, and the arrival of the hijackers in the U.S. In total, the Commission relied on more than 100 interrogation reports produced by the CIA. The second round of interrogations sought by the Commission involved more than 30 separate interrogation sessions.

No one disputes that the interrogations were critical to the Commission’s understanding of the plot.

"What we did is the authoritative basis of knowledge on the interrogations until historians get to ply them years from now," said a former Commission staffer who worked with the CIA on the interrogation reports.

Errors pointed out

One critic of U.S. use of harsh interrogation techniques says that while the Commission Final Report remains credible, it was a mistake to base so much of it on what was retrieved from the interrogation sessions.

Karen Greenberg, director of the Center for Law and Security at New York University’s School of Law, put it this way: "You read it, the story still makes sense, forgetting the interrogations. What matters - who did it, who planned it - looks like the right story. But it should have relied on sources not tainted. It calls into question how we were willing to use these interrogations to construct the narrative."

According to both current and former senior U.S. intelligence officials, the operatives cited by the Commission were subjected to the harshest of the CIA’s methods, the "enhanced interrogation techniques." The techniques included physical and mental abuse, exposure to extreme heat and cold, sleep deprivation and waterboarding.

In addition, officials of both the 9/11 Commission and CIA confirm the Commission specifically asked the agency to push the operatives on a new round of interrogations months after their first interrogations. The Commission, in fact, supplied specific questions for the operatives to the agency. This new round took place in early 2004, when the agency was still engaged in the full range of harsh techniques. The agency suspended the techniques in mid-2004. Agency spokesmen have refused to identify what techniques were used, when they were used or the names of those who were harshly questioned.

Zelikow said the lack of direct access forced the Commission to seek secondary sources and to request the new round of questioning. In the end, says Zelikow, the Commission relied heavily on the information derived from the interrogations, but remained skeptical of it. Zelikow admits that "quite a bit, if not most" of its information on the 9/11 conspiracy "did come from the interrogations."

"We didn’t have blind faith," Zelikow tells NBC News. "We therefore had skepticism. The problems (in getting cooperation from the agency) enforced our concerns about the underlying interrogation.

A former senior U.S. intelligence official says the Commission never expressed any concerns about techniques and even pushed for the new round.

"Remember," the intelligence official said, "The Commission had access to the intelligence reports that came out of the interrogation. This didn't satisfy them. They demanded direct personal access to the detainees and the administration told them to go pound sand.

"As a compromise, they were allowed to let us know what questions they would have liked to ask the detainees. At appropriate times in the interrogation cycle, agency questioners would go back and re-interview the detainees, many of (those) questions were variants or follow ups to stuff previously asked."

Commission staffers interviewed by NBC News do not dispute the official’s assertion that they didn’t ask about interrogation techniques. "We did not delve deeply into the question of the treatment of the prisoners", as one put it. "Standards of treatment were not part of our mission." According to the other, "We did not ask specifically. It was not in our mandate."

The commission first requested access to the detainees early in 2004, around the same time the Abu Ghraib scandal broke. In that scandal, military interrogators at Baghdad’s most notorious prison were accused of torturing low level prisoners. The Commission wanted the access not to check on interrogation techniques or the operatives’ condition, but to get their own access.

Michael Ratner, president of the Center for Constitutional Rights, says he is "shocked" that the Commission never asked about extreme interrogation measures.

"If you’re sitting at the 9/11 Commission, with all the high-powered lawyers on the Commission and on the staff, first you ask what happened rather than guess," said Ratner, whose center represents detainees at Guantanamo. "Most people look at the 9/11 Commission Report as a trusted historical document. If their conclusions were supported by information gained from torture, therefore their conclusions are suspect."

Zelikow says the Commission tried its best to get inside the interrogation process.

"In early 2004, we conducted private interviews with (CIA Director George J.) Tenet. There were three interviews…five or six hours each, involving Zelikow, Kean and Hamilton," said a Commission staffer, referring to the commission director, and co-chairs, former New Jersey Governor Tom Kean and former Indiana congressman Lee Hamilton. "We talked to him about access at that point…Tenet doesn’t say no…the response was ‘Talk to my people."

Tenet’s "people" explained why the commission couldn’t question the operatives.

"The explanation was that the symbiosis between the interrogator and the prisoner would be harmed," added the staffer, "…that introducing external elements could unbalance the relationship. They wanted the prisoners to have total dependency on them…all this psychology."

Although he admits neither he nor his staff asked about interrogation techniques, Zelikow now believes perhaps he should have, that there were reasons for the agency’s lack of cooperation.

"A whole lot needed to be kept from us," he said he now realizes. "It would have revealed a lot of things that it was not in the government’s interest to reveal. They might have worried what we would have learned about the interrogation techniques."

Zelikow adds that one particularly telling position was the agency’s refusal to let the Commission interview the interrogators.

"We needed more information to judge reports we were reading," he said. "We needed information about demeanor of the detainees. We needed more information on the content, context, character of the interrogations."

Current and former agency officials say the commission had enough information to fulfill their mission.

"The CIA went to great lengths to meet the requests of the 9/11 Commission and provided the Commission with a wealth of information," said Mark Mansfield, the CIA’s chief spokesman. "The 9/11 Commission certainly had access to, and drew from, detailed information that had been provided by terrorist detainees. That's how they reconstructed the plot in their comprehensive report."

The former official said that senior intelligence staff feared that if the agency permitted the commission to send staffers to the CIA’s secret prisons to talk with the operatives, the locations of the prisons wouldn’t be secret for very long.

Zelikow agreed that the Commission specifically asked for the new round after reviewing the agency’s first interrogation reports. "That is correct," he said of the rationale for the new round of interrogations. "That was one of the ways they sought to deal with our concerns. They (the first round) had value but were not satisfactory."

"They were looking prospectively in their questioning…looking at current threats. We were looking retrospectively. So we needed the follow-up questions."

The NBC News analysis shows that there were 30 separate interrogation sessions in early 2004 when the second round of questioning began. Based on the number of references attributed to each of the sessions, they appear to have been lengthy.

So why did the Commission ultimately rely so heavily on the interrogations even though some believed there was a possibility of mistreatment?

"Ultimately, we chose to publicly release our understanding of what took place, based on everything we had access to," said Zelikow, adding that the Commission did explain its feelings in a largely ignored explanatory box in the report on the value of the interrogations.

According to the note: "Our access to them (the operatives) has been limited to the review of intelligence reports based on communications received from the locations where the actual interrogations take place. We submitted questions for use in the interrogations, but had no control over whether, when, or how questions of particular interest would be asked."

Ratner argues "if they suspected there was torture, they should have realized that as a matter of law, evidence derived from torture is not reliable, in part because of the possibility of false confession…at the very least, they should have added caveats to all those references."

Fourteen of the highest-value detainees had their initial hearings this spring before the Pentagon’s Combatant Status Review Tribunal. The tribunal acts as sort of a grand jury, charged with determining if a detainee should be held over for trial.

Four of them said they gave information only to stop the torture. Although details were redacted in all the detainees’ testimony, the tribunal permitted the inclusion of a letter from a detainee’s father in one case, citing what he claimed was American torture of his son.

In the letter placed in the record, Ali Khan claims his son, Majid, underwent extensive torture before and after interrogation sessions.

"The Americans tortured him for eight hours at a time, tying him tightly in stressful positions in a small chair until his hands feet and mind went numb. They retied him in a chair every hour, tightening the bonds on his hands and feet each time so that it was more painful. He was often hooded and had difficulty breathing. They also beat him repeatedly, slapping him in the face, and deprived him of sleep.

"When he was not being interrogated, the Americans put Majid in a small cell that was totally dark and too small for him to lie down in or sit in with legs stretched out. He had to crouch. The room was also infested with mosquitoes. This torture only stopped when Majid agreed to sign a statement that he wasn’t even allowed to read. But then it continued when Majid was unable to identify certain streets and neighborhoods in Karachi that he did not know."

Khan, a Pakistani citizen who formerly resided in Maryland, is accused of plotting to carry out terrorist attacks in both Pakistan and the United States and helping al Qaeda operatives enter the United States.

Ironically, two former commission staffers noted that the Commission Final Report essentially recommends that the US encourage an end to torture.

They pointed specifically to a Commission recommendation: "The US government must define what the message is, what it stands for. We should offer an example of moral leadership in the world, committed to treat people humanely, abide by the rule of law, and be generous and caring to our neighbors."

Robert Windrem is an NBC News Producer. Victor Limjoco is an associate producer for NBC Nightly News Online. NBC News intern Ching-Yi Chang also contributed to this report.