Several pilots reported diamondback terrapin turtles on runway 4L during the morning rush hour, Sky News reported citing LiveATC.net.
Airport staff helped clear the creatures, taking them on a pick-up truck to the beach.
JFK is surrounded by a bay and wetland areas. The turtles were trying to get to an ideal location to lay their eggs and chose to cross runway 4L, officials said.
Flights were delayed for around 30 minutes, the Federal Aviation Administration said.
"We built on the area where they were nesting for generations, so we feel incumbent to help them along the way," said a spokesman for the Port Authority of New York and New Jersey.
People began tweeting about the turtles soon after the news broke. JFKTurtles had nearly 3,000 followers on Twitter.
Airline Jet Blue wrote: "Oh @JFKTurtles, we could never stay mad at you... Glad you made it to your honeymoon spot safe."
This was not the first time turtles have invaded the JFK. In 2009, 78 turtles emerged suddenly at the runways, the spokesman said.
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