The 10-member commission said it had learned through interviews that the agency had not turned over tapes, statements, reports and other documents "highly material to our inquiry."
One commission member said the documents relate in part to lingering questions over how, and how quickly, the FAA notified U.S. air defenses about hijacked planes on Sept. 11, 2001.
The FAA, which earlier told the panel it had provided everything, turned over additional material in the last few days and pledged to cooperate. But the commission said the delay "has significantly impeded the progress of our investigation and undermined our confidence in the completeness of the FAA's production."
The commission, made up of five Democrats and five Republicans, voted to issue the subpoena Tuesday night after completing a public hearing on intelligence reforms.
"This disturbing development at one agency has led the commission to re-examine its general policy of relying on document requests rather than subpoenas," the panel said in a statement.
FAA spokesman Greg Martin said the agency has worked closely with the commission from the beginning and was surprised at the decision to issue a subpoena. He said the FAA followed established procedures for investigations, but now recognizes they were not satisfactory in this case.
"No documents were ever knowingly withheld from the commission," Martin said.
The subpoena is the first issued by the National Commission on Terrorist Attacks Upon the United States. For months, some relatives of Sept. 11 victims have urged the commission to use its subpoena power to demand important documents.
Other agencies should be on notice that they should consider requests for documents as seriously as they would a subpoena, the panel said.
The commission's report is due May 27, 2004. For the first time, the panel suggested that fights over documents might make it unable to meet that deadline.
During a hearing in May, Democratic commissioner Richard Ben-Veniste, a former Watergate prosecutor, dug into the length of time it took the FAA to notify the North American Aerospace Defense Command about American Airlines Flight 77 between the time the plane deviated from its flight path to the time it crashed into the Pentagon.
The FAA knew that Los Angeles-bound Flight 77 left its course at 8:55 a.m., Ben-Veniste said, but NORAD did not get official notice of a hijacking until 9:24 a.m. A witness at the hearing, retired Maj. Gen. Larry K. Arnold, who was in charge of NORAD on the day of the attacks, said it was "physically possible" that fighter jets could have beaten the civilian airliner to the Pentagon had they been activated earlier.
Ben-Veniste said Wednesday that the FAA material in question is relevant to that line of inquiry.
"It has to do with the events of the day, and what notifications were given, be they formal, informal, delayed or in real time," he said. "That's quite important to reconstructing the events of the day."
Ben-Veniste also said the commission's vote to issue the subpoena was unanimous.
The panel's chairman, former New Jersey Gov. Thomas Kean, a Republican, said it is possible the FAA's most recent delivery contained all the documents the commission needs. "But given our experience with the agency in the past," he said, "we thought a subpoena was justified."
Stephen Push, a director of Families of September 11, welcomed the news of the first subpoena and said he hoped others will follow. He said he believes some government agencies are "hoping to escape scrutiny" by withholding information from the commission.
This is not the first time the panel has raised alarms over its access to evidence. In July, committee members complained of stonewalling by the CIA and the departments of Defense, Homeland Security and Justice.
By Laurence Arnold