It happened around 6 a.m. at a TSA PreCheck checkpoint at Terminal 5, according to agency spokesman Joe Pentangelo.
Three of the 11 passengers who walked through the security gate set off metal detectors, NBC New York reported.
The travelers' carry-on bags received the required screening, according to NBC New York.
Port Authority police were not notified until 8 a.m. when a TSA supervisor discovered the security breach. It's unknown how it was discovered.
Officials were unable to find the 11 travelers before they were believed to have boarded their flights, the spokesman said.
Police were able to identify three people who got on a flight to California, where they will be screened on arrival, according to the Port Authority.
"Port Authority Police are continuing to assist federal authorities in efforts to identify and locate the other eight passengers," Pentangelo said in an email statement.
A TSA spokesman did not immediately respond to request for comment.