The officer, Lt. Col. Anthony Shaffer, said military lawyers later blocked the team from sharing any of its information with the bureau.
Colonel Shaffer said in an interview on Monday night that the small, highly classified intelligence program, known as Able Danger, had identified the terrorist ringleader, Mohamed Atta, and three other future hijackers by name by mid-2000, and tried to arrange a meeting that summer with agents of the Washington field office of the Federal Bureau of Investigation to share its information.
But he said military lawyers forced members of the intelligence program to cancel three scheduled meetings with the F.B.I. at the last minute, which left the bureau without information that Colonel Shaffer said might have led to Mr. Atta and the other terrorists while the Sept. 11 attacks were still being planned.
"I was at the point of near insubordination over the fact that this was something important, that this was something that should have been pursued," Colonel Shaffer said of his efforts to get the evidence from the intelligence program to the F.B.I. in 2000 and early 2001.
He said he learned later that lawyers associated with the Special Operations Command of the Defense Department had canceled the F.B.I. meetings because they feared controversy if Able Danger was portrayed as a military operation that had violated the privacy of civilians who were legally in the United States.
"It was because of the chain of command saying we're not going to pass on information - if something goes wrong, we'll get blamed," he said.
The Defense Department did not dispute the account from Colonel Shaffer, a 42-year-old native of Kansas City, Mo., who is the first military officer associated with the program to acknowledge his role publicly.
At the same time, the department said in a statement that it was "working to gain more clarity on this issue" and that "it's too early to comment on findings related to the program identified as Able Danger." The F.B.I. referred calls about Colonel Shaffer to the Pentagon.
The account from Colonel Shaffer, a reservist who is also working part time for the Pentagon, corroborates much of the information that the Sept. 11 commission has acknowledged it received about Able Danger last July from a Navy captain who was also involved with the program but whose name has not been made public. In a statement issued last week, the leaders of the commission said the panel had concluded that the intelligence program "did not turn out to be historically significant."
The statement said that while the commission did learn about Able Danger in 2003 and immediately requested Pentagon files about it, none of the documents turned over by the Defense Department referred to Mr. Atta or any of the other hijackers.
Colonel Shaffer said that his role in Able Danger was as liaison with the Defense Intelligence Agency in Washington, and that he was not an intelligence analyst. The interview with Colonel Shaffer on Monday was arranged for The New York Times and Fox News by Representative Curt Weldon, the Pennsylvania Republican who is vice chairman of the House Armed Services Committee and a champion of data-mining programs like Able Danger.
Colonel Shaffer's lawyer, Mark Zaid, said in an interview that he was concerned that Colonel Shaffer was facing retaliation from the Defense Department, first for having talked to the Sept. 11 commission staff in October 2003 and now for talking with news organizations.
Mr. Zaid said that Colonel Shaffer's security clearance was suspended last year because of what the lawyer said were a series of "petty allegations" involving $67 in personal charges on a military cellphone. He said that despite the disciplinary action, Colonel Shaffer had been promoted this year from major.
Colonel Shaffer said he had decided to allow his name to be used in part because of his frustration with the statement issued last week by the commission leaders, Thomas H. Kean and Lee H. Hamilton.
The commission said in its final report last year that American intelligence agencies had not identified Mr. Atta as a terrorist before Sept. 11, 2001, when he flew an American Airlines jet into one of the World Trade Center towers in New York.
A commission spokesman did not return repeated phone calls on Tuesday for comment. A Democratic member of the commission, Richard Ben-Veniste, the former Watergate prosecutor, said in an interview on Tuesday that while he could not judge the credibility of the information from Colonel Shaffer and others, the Pentagon needed to "provide a clear and comprehensive explanation regarding what information it had in its possession regarding Mr. Atta."
"And if these assertions are credible," Mr. Ben-Veniste continued, "the Pentagon would need to explain why it was that the 9/11 commissioners were not provided this information despite requests for all information regarding Able Danger."
Colonel Shaffer said he had provided information about Able Danger and its identification of Mr. Atta in a private meeting in October 2003 with members of the Sept. 11 commission staff when they visited Afghanistan, where he was then serving. Commission members have disputed that, saying that they do not recall hearing Mr. Atta's name during the briefing and that the name did not appear in documents about Able Danger that were later turned over by the Pentagon.
"I would implore the 9/11 commission to support a follow-on investigation to ascertain what the real truth is," Colonel Shaffer said in the interview this week. "I do believe the 9/11 commission should have done that job: figuring out what went wrong with Able Danger."
"This was a good news story because, before 9/11, you had an element of the military - our unit - which was actually out looking for Al Qaeda," he continued. "I can't believe the 9/11 commission would somehow believe that the historical value was not relevant."
Colonel Shaffer said that because he was not an intelligence analyst, he was not involved in the details of the procedures used in Able Danger to glean information from terrorist databases, nor was he aware of which databases had supplied the information that might have led to the name of Mr. Atta or other terrorists so long before the Sept. 11 attacks.
But he said he did know that Able Danger had made use of publicly available information from government immigration agencies, from Internet sites and from paid search engines like LexisNexis.