Transportation Security Administration chief Kip Hawley told the Senate Commerce Committee Thursday that he has directed that the program's information technology system "go through a comprehensive audit."
Hawley did not say whether any security flaws or breaches had been discovered.
"We don't believe any passenger information has been compromised," Amy von Walter, spokeswoman for TSA, told reporters.
The program called Secure Flight has been troubled from the start.
It is strongly opposed by civil libertarians who fear the program would grow into a massive domestic surveillance system in which the government tracks people whenever they travel.
The time-out for this very troubled program came after yet another audit by congressional watchdogs found the system just isn't ready for prime time, CBS News correspondent Bob Fuss reports.
The government has already spent more than $200 million trying to replace the system used now, in which airline employees compare the names of ticket buyers to an incomplete and often incorrect "no fly" list.
Under Secure Flight, the government would take over from the airlines the task of checking names against watch lists.
The Sept. 11 commission later urged the administration to expedite the task because, it said, the watch lists currently used by airlines aren't complete.
But checking names against watch lists hasn't been as easy as it sounds, partly because airlines collect only limited information about passengers.
Also, the number of names on the watch lists increased into the tens of thousands since the Sept. 11 attacks. That problem has resulted in passengers from infants to Sen. Edward M. Kennedy being mistakenly told they couldn't fly because they have the same name as someone on the watch list.
The project has also drawn protests from privacy advocates and civil libertarians because its stated purpose has changed, often expanding.
Project managers once said that it would be used to track down violent criminals, and then backed down. They've also proposed using commercial data, such as that supplied by Choicepoint, to locate members of terrorist sleeper cells among people who buy airline tickets.