Are many of the secrets of 9/11 still hidden in top-secret government files?

Almost certainly, say former staff members of the 9/11 Commission. With the nation scheduled to mark the ninth anniversary of the terrorist attacks this weekend, former staffers tell The Daily Beast it is clear that the 9/11 Commission, which went out of business in 2004, failed to conduct a thorough inspection of the government's most important library of raw intelligence on al Qaeda and the 9/11 plot. And nobody appears to have inspected that intelligence since.

The archives, maintained by the National Security Agency at its headquarters in Fort Meade, Maryland, were reviewed—in a cursory fashion—only in the final days of the commission's investigation, and then only because of last-minute staff complaints that the NSA's vast database was being ignored.

• Bruce Riedel: Al Qaeda’s Post-9/11 Surge• Full Coverage of the 9/11 anniversaryThroughout its investigation, staffers complained, the commission's leaders were fixated on what could be found in the terrorism files of the CIA and the FBI, the two big targets for criticism in the panel's final report, and largely ignored the NSA, the government's chief eavesdropping agency.

When the commission did get into the NSA archives during a frantic, down-to-the-wire weekend search in June 2004, it found explosive material suggesting links between the 9/11 plotters and the government of Iran and the Iranian-backed Hezbollah militants of Lebanon. The Iran material was forced into the commission's final report with limited context and without any chance for followup by the commission; the panel was about to shut down. (I revealed much of this in my 2008 book, The Commission: The Uncensored History of the 9/11 Investigation.)

"It's always been frightening to me to consider what is still at the NSA, whatever we never had time to see," said a former commission staff member, who now works elsewhere in the federal government and is barred from speaking to the press for attribution. "It's kind of shocking to me that no one has tried to get back in there since. We certainly didn't see everything at NSA."

“It’s always been frightening to me to consider what is still at the NSA, whatever we never had time to see,” said a former commission staff member.

Former staffers say they do not mean to suggest that unseen NSA archives will support any of the more far-fetched conspiracy theories about 9/11—especially the idea that the 9/11 attacks were some sort of "inside job" by the Bush administration.

Full coverage of the 9/11 anniversaryBut they say there may well be evidence at the agency to suggest closer ties than have been previously disclosed between al Qaeda and foreign governments, and that the government had far more explicit warnings of an imminent terrorist attack in 2001.

There is no sign that anyone from Capitol Hill or elsewhere in the government has attempted to get back into the NSA to review its pre-9/11 terrorism archives, even though they are—without doubt—the most complete library on earth of intercepted communications between al Qaeda and its followers, including several of the 9/11 hijackers, and its foreign sponsors.

The NSA said in a statement to The Daily Beast that it had "fully supported" the 9/11 Commission "and provided access to its facilities, documents, personnel, and resources in support" of its investigation. Agency officials had no comment, however, when asked if the NSA was concerned that its archives were not adequately reviewed by the commission, or whether other groups had since reviewed the material.

Spokesmen for the House and Senate intelligence committees did not respond to similar questions.

In terms of budget, the NSA is the nation's largest spy agency, spending tens of billions of dollars a year on eavesdropping satellites and ground-based intercepts, much of it devoted to listening in on phone calls and intercepting emails among terrorists and their allies. The raw intelligence gathered from the intercepts is then shared with the CIA and other agencies for analysis.

Former Sen. Bob Graham of Florida, a Democrat who led a joint congressional investigation of 9/11 that predated the formation of the 9/11 Commission, tells The Daily Beast he had been aware that the commission might have missed so much evidence at the NSA.

"The NSA was providing well over half of the raw intelligence that the intelligence community was getting at that time," he said.

Graham said he worried, in particular, that the commission may have missed other evidence at the NSA of foreign support for al Qaeda; the congressional investigation turned up evidence that some officials of the government of Saudi Arabia, including a Saudi diplomat based in Los Angeles, may have provided assistance to the 9/11 hijackers after they arrived in the U.S.

John R. Schindler, a former NSA intelligence analyst who is now a professor of national-security affairs at the U.S. Naval War College, said he would urge congressional investigators and others to review the material at the NSA that the 9/11 Commission missed. He said he was baffled that the archives had not been thoroughly inspected at the time.

"For decades, it's been by far the biggest source of intelligence in the U.S. government," he said of the NSA. "A very high percentage of the terrorism cases that appear in the media begin with the NSA intercepting information."

What might the 9/11 Commission have missed?

"You won't know until you look," he said. "It's important to remember that when access was given to the archives of the NSA's predecessor agency during World War II, the whole history of World War II had to be rewritten." He was referring to the disclosure—decades after the war—that the United States and its allies had broken Nazi codes, explaining allied victories that had previously been attributed solely to the genius of American military leaders.

Philip Shenon is an investigative reporter based in Washington D.C. He was a reporter at The New York Times from 1981 until 2008. He left the paper in May 2008, a few weeks after his first book, The Commission: The Uncensored History of the 9/11 Investigation , hit the bestsellers lists of both The New York Times and The Washington Post. He has reported from several warzones and was one of two reporters from the Times embedded with American ground troops during the invasion of Iraq in the 1991 Gulf War.