WASHINGTON – An Army intelligence officer said yesterday he told staff members from the September 11 commission that a secret military unit had identified two of the three cells involved in the 2001 terrorist strikes more than a year before the attacks.

Lieutenant Colonel Anthony Shaffer, who said he was associated with the “Able Danger” unit, said that during a 2003 meeting in Afghanistan, he mentioned that the unit had identified September 11 ringleader Mohamed Atta along with three other hijackers as terrorist suspects.

The commission has denied that Attas’s name or the name of any future hijackers were mentioned during the meeting.

Three months later, in January 2004, Colonel Shaffer said he was back in America and offered to follow up with the commission, but his offer was declined.

“I just walked away shocked that they would kind of change their mind, but I figured someone with equal or better knowledge …probably came and talked to them, so they must’ve taken care of it,” Colonel Shaffer said.

Colonel Shaffer said he was told the commission obtained only two briefcase-size loads of documents from at least 15-plus boxes of information on Able Danger.

Lieutenant Colonel Chris Conway, a Pentagon spokesman, said yesterday an investigation into Able Danger was under way.

The department “has been working to gain more clarity on this issue. Accordingly, we continue to interview a number of individuals associated with Able Danger,” Colonel Conway said.

Colonel Conway said it was too soon to comment on findings related to the program.

Al Felzenberg, spokesman for the commission’s follow-up project, said the commission is awaiting the results of the Pentagon’s investigation.

A statement last Friday by former commission chairman Thomas Kean and vice chairman Lee Hamilton said the commission did not obtain enough information on the operation to consider it historically significant.

Colonel Shaffer said Able Danger identified Atta and three other September 11 hijackers in 2000, but that military lawyers stopped the unit from sharing the information with the FBI out of concerns about the legality of gathering and sharing information on people in America.

“The lawyers’ view was to leave them alone, they had the same basic rights as a U.S. citizen, a U.S. person, and therefore the data was kind of left alone,” Colonel Shaffer said.

Colonel Shaffer said he and a Navy officer disagreed with that and tried to set up meetings with the FBI, but each time the idea was rejected by lawyers from the Special Operations command.

“There was a feeling … if we give this information to the FBI and something goes wrong, we’re going to get blamed for whatever goes wrong,” Colonel Shaffer said.

The statement by Messrs. Kean and Hamilton said only Atta was mentioned to them as being identified by Able Danger. They were told by a Navy officer about Atta 10 days before the commission released its report in July 2004, but the officer did not have documentation to back it up, the statement said.

The statement also said the Navy officers dates related to the pre-September 11 whereabouts of Atta did not fit with what they knew.

Colonel Shaffer said it did not surprise him the dates would be different.

Able Danger “wasn’t about dates and locations. It was about associations and linkages. That’s what the focus was,” Colonel Shaffer said.

Colonel Shaffer said Able Danger identified the terrorists using data-mining techniques. His relationship to Able Danger was first reported Tuesday night by the New York Times and Fox News Channel.

Colonel Shaffer’s lawyer, Mark Zaid, said yesterday that Colonel Shaffer does not have documentation related to Able Danger because his security clearance was suspended in March 2004 because of “petty and frivolous” reasons. They include a dispute over mileage reimbursement and a charge for personal calls on a work cell phone, Mr. Zaid said.

Colonel Shaffer, an Army reservist, has been on paid administrative leave for the past 16 months, Mr. Zaid said. He was an active Army major during his involvement with Able Danger, Mr. Zaid said.

Several defense officials yesterday identified the Navy officer as Captain Scott Phillpott. They discussed matters related to Able Danger only on the condition of anonymity because of the sensitive nature of the program and the investigation into it.

A Navy spokesman said Captain Phillpott was declining requests to speak with reporters.

Rep. Curt Weldon, a Republican of Pennsylvania and vice chairman of the House Armed Services and Homeland Security committees, has said the September 11 commission did not adequately investigate the claim that four of the hijackers had been identified more than a year before the attacks.