The commission has decided to subpoena the US military's North American Aerospace Defence Command (NORAD) records for information it promised but did not deliver.
It will be the second subpoena issued by the commission which has complained of delays by some government agencies in providing information needed to complete the investigation by a May deadline.
The commission subpoenaed the Federal Aviation Administration in October, accusing it of slowing the probe by not providing timely and complete information.
The panel in May requested information on air traffic control tracking of hijacked aircraft and the agency's communication with NORAD, the US-Canadian military alliance that scrambled fighter jets during the attacks.
Some members of the commission are interested in the time sequence for notifying the jets that headed to Washington where one of the hijacked planes struck the Pentagon.
"The commission has encountered some serious delays in obtaining needed documents from the Department of Defence," the panel said in a statement.
"We are especially dismayed by problems in the production of the records of activities of the North American Aerospace Defence Command (NORAD) and certain Air Force commands on September 11, 2001," it said.
"The commission has therefore voted to issue a subpoena requiring the production of these records," the statement said.
President Bush said last week that he was willing to give the commission limited access to only a portion of the daily intelligence reports given to him before the attacks.
Stephen Cambone, defence undersecretary for intelligence, said Defence Secretary Donald Rumsfeld expected the department to comply with schedules for document submissions.
"The commission has a statutory deadline it must meet," Cambone said. "And the secretary has directed that the department be responsive to help ensure the commission can meet its deadlines."
The 10-member National Commission on Terrorist Attacks Upon the United States is examining lapses in national security related to the September 11 attacks that killed about 3000 people.
The commission has also previously said it may subpoena the White House to gain access to intelligence reports given to the president if that information was not turned over.
President George Bush has been reluctant to disclose what he had been told. He said last week that he was willing to give the commission limited access to only a portion of the daily intelligence reports given to him before the attacks.