Lt. Col. Tony Shaffer (search), a military intelligence specialist who worked on a secret pre-Sept. 11 investigative unit called Able Danger (search), has gone on the record, telling FOX News that he personally briefed staffers with the Sept. 11 commission in October 2003 about Mohamed Atta.

A statement from the commission — formally known as the National Commission on Terrorist Attacks Upon the United States — said that three staffers attended the meeting, but none, including Executive Director Phil Zelikow, remembers Shaffer mentioning Atta.

Still, the intelligence agent is standing by his claim that he told them that the lead hijacker in the Sept. 11, 2001, terror attacks had been identified in the summer of 2000 as an Al Qaeda operative living in the United States.

"What we talked about to the Sept. 11 commission was we found that these guys matched a pattern, a pattern, which in this case with Atta and the other four terrorists, matched the Brooklyn location," Shaffer said in his first television interview.

He said the intelligence unit used algorithms based on many items of information that popped out patterns that linked individuals to a group or location. The other three terrorists linked were Khalid al-Mihdhar (search), Nawaf al-Hazmi (search) and Marwan al-Shehhi (search).

Shaffer's briefing with the staffers took place in Bagram, Afghanistan. A Sept. 11 commission spokesman said the commission made two broad requests to the Pentagon for information relating to Able Danger, but received nothing to back up Shaffer's claim.

"None of the documents turned over to the commission mention Mohamed Atta or any of the other future hijackers," the spokesman said. Shaffer said the commission never received the whole story.

"I'm told confidently by the person who moved the material over, that the Sept. 11 commission received two briefcase-sized containers of documents. I can tell you for a fact that would not be one-twentieth of the information that Able Danger consisted of during the time we spent" investigating, Shaffer said.

Shaffer said in the late summer of 2000, he tried three times to set up meetings between the FBI's Washington field office and officials with Able Danger who believed the information about Atta should be shared with domestic law enforcement.

Michael Mason, head of the FBI field office, said it's possible the meetings were arranged, but that cannot be verified by any means.

It is "premature at best to suggest that the information gathered at such a meeting would have prevented the events of Sept. 11," Mason added.

Shaffer said each of the meetings was cancelled on short notice — by members of the special operations command.

"On these occasions when we had set up these meetings between the FBI and special operations command, special operations command pulled out of all three. They decided not to show up," he said.

Shaffer said the meetings were canceled for a variety of reasons, including concern about the military investigating individuals who were in this country legally. Some of the hijackers had valid visas. They also were concerned that if any fallout came from the FBI's activities, the special operations people feared they would take the hit.

According to two sources, Able Danger was set up in the late 1990s to track Usama bin Laden's terror network worldwide. Shaffer said its omission from the final Sept. 11 commission report makes it a "partial record."

"Leaving out a project targeting Al Qaeda as a global threat a year before we're attacked by Al Qaeda is equivalent to having an investigation into Pearl Harbor and leaving, somehow, out the Japanese," Shaffer said.

FOX News has learned that Shaffer's security clearance was suspended last year over a disputed phone bill and allegations that he had not gone through the proper chain of command to obtain an award for Able Danger. Shaffer's lawyer told FOX News that no formal action has ever been taken against Shaffer — and since then he was promoted by the Army to lieutenant colonel.

A military spokesman told FOX News that the Pentagon wants more clarity on the issue and continues to interview those involved. Shaffer said he has now spoken with senior defense officials.

FOX News' Catherine Herridge contributed to this report.