Airport workers say there are about six cat colonies at the airport, The New York Post reported. They are believed to be descended from fugitives who escaped while being transported by air and from released pets.
For years, many employees have treated the cats as pets, putting out canned food for them.
Narine Sripasad, who drives an airport shuttle bus, said about 20 cats live in his depot under the engine room.
"Some of the guys call them and pet them," he said. "They are not scared. They're friendly."
The Port Authority of New York and New Jersey plans to trap the animals and turn them over to Animal Care and Control. That means most are likely to end up being euthanized and that has cat lovers up in arms.
The New York City Feral Cat Initiative offered to trap the cats, neuter them, give away the adoptable ones and return the others to the airport. But the Port Authority, which said the cats are a safety issue, rejected the plan.