The TSA declined to provide complete information on how individuals are selected for Quiet Skies and how the programme works.
According to the TSA, the programme used travel records and other factors to identify passengers who will be subject to additional checks at airports and, sometimes, be observed in flight by air marshals who report on their activities to the agency.
The initiative raises new questions about the privacy of ordinary Americans as they go about routine travel within the United States and about the broad net cast by law enforcement as it seeks to keep air travel safe.
Gregory said the programme did not single out passengers based on race or religion and should not be considered surveillance because the agency does not, for example, listen to passengers' calls or follow flagged individuals around airports.
But during in-flight observation of people who are tagged as Quiet Skies passengers, marshals use an agency checklist to record passenger behaviour: Did he or she sleep during the flight? Did he or she use a cellphone? Look around erratically?
"The programme analyses information on a passenger's travel patterns while taking the whole picture into account," Gregory said, adding "an additional line of defence to aviation security."
"If that person does all that stuff, and the airplane lands safely and they move on, the behaviour will be noted, but they will not be approached or apprehended," Gregory said.
He declined to say whether the programme has resulted in arrests or disruption of any criminal plots.
Hugh Handeyside, senior staff lawyer with the American Civil Liberties Union's National Security Project, called on the TSA to provide more information about the programme to passengers.
"Such surveillance not only makes no sense, it is a big waste of taxpayer money and raises a number of constitutional questions," he said.
"These concerns and the need for transparency are all the more acute because of TSA's track record of using unreliable and unscientific techniques to screen and monitor travellers who have done nothing wrong."
The TSA, which was created soon after the September 11, 2001 terrorist attacks, screens on average more than two million passengers a day.
While the agency is tasked with a weighty public safety mission, it has at times been publicly rebuked for being intrusive and abusive at airport checkpoints. It has been accused of doing little to enhance security while subjecting passengers to searches or questioning.
In 2015, the Department of Homeland Security's inspector general found that undercover agents were able to slip fake bombs past TSA screeners about 95 per cent of the time. A year later, the flying public was in an uproar over long lines to move through security screening.
But TSA officials have said that ensuring public safety while keeping passengers moving has made their work difficult.
"We have a no-fail mission," former TSA administrator Peter Neffinger told Congress in 2015.
The agency has also been criticised for its treatment of Muslims and other minorities who have complained of being profiled while travelling.
Earlier this year, media reports revealed that the agency had compiled a secret list of unruly passengers.
Passengers may be selected for Quiet Skies screening because of their affiliation with someone on the Government's no-fly list or other databases aimed at preventing terrorist attacks.
"This programme raises a whole host of civil liberties and profiling concerns," said Faiza Patel, co-director of the New York University School of Law's Brennan Centre for Justice.
Critics say the TSA's databases are overly broad and include incorrect information.
The no-fly list, for example, grew from about 16 people in September 2001 to 64,000 people in 2014.
But Patel, a lawyer, said that law enforcement officials are generally free to surveil individuals as long as they do not do so based on criteria such as ethnicity.
