(CNN) -- All passengers flying within or to the United States are now being screened against government watch lists before they get their boarding passes, the Department of Homeland Security announced Tuesday.
The Transportation Security Administration achieved the target a month ahead of schedule, the department said in a statement.
Screening all passengers was a key recommendation of the 9/11 Commission.
But screening programs have been mired in controversy, with privacy advocates and civil liberties campaigners objecting to aspects of earlier plans.
The program now up and running is known as Secure Flight. It replaces an ad hoc system, where airlines do the screening, with a government-run program.
It screens passengers against lists of known or suspected terrorists. It is unable to stop terrorists whose names are not on government watch lists.
"Obviously, (alleged Christmas Day bomber Umar Farouk) Abdulmutallab was not in the terrorist screening database, so Secure Flight would not apply," TSA head John Pistole conceded Tuesday.
It also wouldn't have caught September 11 hijacker Mohammed Atta or shoe bomber Richard Reid, aviation security expert Rafi Ron told CNN.
But Pistole said the new system is still an improvement. It will, for example, rely on lists updated automatically every two hours, so it would have identified failed Times Square bomber Faisal Shahzad, who tried to flee the country.
Pistole also hopes Secure Flight will cut down the number of people incorrectly being identified as terrorists.
"Six months from now if we don't see any reduction, that would concern me. But right now we're just cautiously optimistic," he said, saying the program had not been running long enough to judge whether it was cutting false positives.
Passengers will have to give their full name, date of birth and gender under Secure Flight, Homeland Security said. Previously, they only had to supply their names.
The department predicted that 99 percent of passengers would be able to print their own bording passes, while the remaining one percent will be further screened, questioned by law enforcement, or barred from boarding the plane.
CNN's Jeanne Meserve and Mike Ahlers contributed to this report.