Marshals will continue to track and monitor those who identify them as interested parties, but they are changing the threshold for reporting their observations to intelligence agencies, according to the TSA.
If a person does nothing remarkable on the flight, the marshal will not send a so-called after-action report, the agency says.
The TSA responded by defending Quiet Skies and told CNN it had "evolved".
"The only change to the program was the reporting mechanism," the agency said.
Sen. Ed Markey, a Massachusetts Democrat who is a critic of the program, said on Monday he was "pleased that the TSA is now putting off its collection of personal information about innocent Americans and their behavior."
"However, I still have concerns about the effectiveness and invasiveness of this program," Markey said.
Critics of the program said that secrecy increases the potential to target people based on their race or nationality. The TSA has said that this is not the case.
The American Civil Liberties Union said that after the program was revealed, it raises "a number of disturbing issues".
In addition to constitutional concerns, "state law enforcement agencies should not detect and monitor travelers and then record detailed information about them without believing that they have done anything wrong," ACLU lawyer Hugh Handeyside wrote in July.
"The safety and security of travelers remains the primary concern of TSA, and Quiet Skies adds another level of security to accomplish this mission," spokeswoman Jenny Burke said in a statement on Monday . She said the agency "continuously reviews each action, making adjustments to optimize effectiveness or respond to emerging threats."
In August, the Inspector General of Homeland Security announced to review the program.