The Port Authority says a water pipe that feeds the terminal's sprinkler system broke at about 2 p.m. Sunday, causing water to flood the terminal.
In a statement, Port Authority Executive Director Rick Cotton said the break "appeared to be weather-related" and called it "unacceptable."
Power in the affected area of the terminal was temporarily shut off for safety reasons. The Port Authority said it was deploying additional staff and providing buses to assist travelers.
The airport is currently experiencing departure and arrival delays of more than two hours.
International arrivals to one terminal at New York's Kennedy Airport have been suspended following a water main break.
More delays have been added Sunday to the storm-related aftermath the already beleaguered airport is working to recover from.
The Port Authority of New York and New Jersey says passengers who have already arrived are being taken to other terminals for processing. Departures were not impacted.
It was unclear what caused the water problem, which sent about 3 inches of it into the terminal's west end. Video shows streams cascading from a ceiling and people slogging through pools of water.
The airport was experiencing arrival delays of more than two hours.
Following the storm, passengers were kept on planes and waited hours to retrieve luggage as flights were delayed and canceled.
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