The bones were found by Port Authority maintenance workers in a secure area of the airport around 6:20 p.m.
The workers were removing high weeds that obscure the sightlines when they made the discovery.
The remains had to be removed before high tide came in.
The area is on the shore line of Flushing Bay, where there is no public access.
The Medical Examiner's office removed the skeletal remains and took them to a lab for analysis.
Port Authority investigators will look into missing persons in the area as they try to determine the identity.
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