The "Quiet Skies" programme reportedly uses an unknown algorithm to flag flyers without any criminal record for surveillance on domestic flights.
Air marshals tasked with carrying out surveillance have pushed back against the programme, according to US media.
TSA denies any racial profiling and says it is a "practical" method.
"With routine reviews and active management via legal, privacy and civil rights and liberties offices, the programme is a practical method of keeping another act of terrorism from occurring at 30,000 feet," the agency said to the BBC in a statement.
What is the programme?
Under "Quiet Skies", federal air marshals have been shadowing travellers on their flights and reporting any suspicious behaviour to TSA, the Boston Globe first reported on Sunday.
These travellers - who are in some cases American citizens - are not part of terrorist screening databases nor are they suspected of any wrongdoings, according to the newspaper.
Travellers are not notified when they have been added to the "Quiet Skies" list, which US media report contains fewer than 50 people.
The programme had been a previously undisclosed TSA operation, but has been in place since 2010.