"The 19 hijackers on 9/11 did some pre-operational flights to assess security," Pistole said.
He said the agency utilised the FBI's terrorist screening database to single out those people who still were permitted to fly. It also stationed plainclothes personnel in airport terminals and as in-flight air marshals to observe passengers.
"For the unknowns it was just based on their behaviour, their activity," he said. "Shame on us if we're doing pre-operation surveillance on the flight, but they weren't on anybody's radar."
Pistole said he consulted with legal counsel at the TSA and the Department of Homeland Security before launching the programme. Congress was unaware of Quiet Skies until reports surfaced over the weekend in a story broken by the Boston Globe and confirmed by the Washington Post.
"It's one thing to provide additional security screening at the checkpoint, but shouldn't we be able to do something more during the flight, just to make sure that we're buying down risk the best way we can?" Pistole said. "We were trying to be forward-leaning and a little more predictive in what the threats might be."
The TSA screens more than two million passengers daily at 440 airports, employing a security force of 43,000 people.
Several members of Congress said yesterday that they were seeking more information on Quiet Skies.
Frederick Hill, spokesman for the Senate Commerce, Science and Transportation Committee, which has jurisdiction over the TSA, said that committee also has requested additional information on the programme.
TSA undercover agents are trained to observe passengers waiting to board flights and those already on the plane, using a lengthy checklist of behaviours that, officials say collectively, suggest the person might be a terrorist.
"It's a programme where we identify people who have irregular travel patterns or exhibit behaviours that we know known terrorists have exhibited, so they come up as someone who is worth additional attention," TSA spokesman Jim Gregory said. "It's no different than how a police precinct might put additional police presence on a beat just to make sure that if anything happens there's someone close by who can address it."
Pistole said he did not know whether anyone had been taken into custody as a result of Quiet Skies.