The pilot of United Airlines 61, a Boeing 767 aircraft, reported at about 9 a.m. that an indicator in the cockpit alerted to a possible mechanical issue.
The FAA said that after the aircraft taxied off the runway and onto a holding area, the pilot reported that the aircraft had "hot brakes" due to the quick stop.
The flight was bound for Honolulu.
The Port Authority dispatched Aircraft Rescue and Firefighter units to the scene and applied water to the brakes.
The situation was reported to be under control shortly before 9:30.
A Port Authority spokesman said passengers were deplaned via a stair truck and two buses were on hand to escort passengers back to Terminal C.
An aircraft tug was sent to the scene to assist in plane removal.
No injuries were reported.