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.
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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.
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An aircraft tug was sent to the scene to assist in plane removal.
No injuries were reported.