The Port Authority said that at 11 a.m., when officials were conducting a daily morning inspection of LGA's airfield, crews found a sinkhole near Runway 4/22.
This is one of the airport's two runways.
Officials shut down the runway and emergency construction and engineering crews arrived on site to determine the cause, but more importantly make repairs.
LaGuardia is known to have one of the tightest schedules with planes landing almost every one to three minutes.
The airport is currently under a ground delay, with flights departing to LGA delayed an average of 98 minutes and 17% of flights have already been canceled.
"Travelers should expect delays and cancellations, particularly with forecast thunderstorms expected later today, and are strongly encouraged to check directly with their airlines for the latest flight status information," Port Authority said.
The runway is expected to be closed through at least 6 a.m. Thursday. The FAA said that is subject to change and it could be impacted by weather.
(ABC News contributed to this report.)
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