An undisclosed federal program called "Quiet Skies" has armed air marshals gathering intelligence on thousands of Americans at airports and on airplanes, according to a Boston Globe report published this weekend.

Meant to thwart emerging threats, the Transportation Security Administration program flags people who aren't already under investigation or on the FBI's Terrorist Screening Database and has agents monitor them for behavior like having an "Adam's apple jump," a "cold penetrating stare" or sweaty palms, tracking dozens of them every day on domestic flights, according to the report. Citing agency documents, it said that all U.S. citizens arriving in the country are screened under Quiet Skies, but travelers being monitored are not notified.

The Globe reported that dozens of air marshals have raised concerns about the program internally — one texted colleagues that the activities are "troubling and raising some serious questions as to the validity and legality of what we are doing and how we are doing it."

The TSA acknowledged to NBC News that the program exists but said it's "not intended to surveil ordinary Americans" or factor in race or religion in its judgments.

"In the world of law enforcement, this program's core design is no different than putting a police officer on a beat where intelligence and other information presents the need for watch and deterrence," a TSA representative said in a statement, claiming there is "robust oversight."

While the report said the initiative began in March, senior government officials told NBC News it dates back to 2010 and that the screening process has evolved.

The American Civil Liberties Union called the program nonsensical, wasteful and concerning on constitutional grounds.

"Given TSA's track record of using unreliable and unscientific techniques to screen and monitor travelers who’ve done nothing wrong, we should remain especially vigilant," the organization tweeted Sunday.