"We ceded to Mother Nature," said Ron Marsico, a spokesman for the Port Authority of New York and New Jersey, which owns the airport.
Workers from the Port Authority and the U.S. Department of Agriculture were scooping up turtles and moving them across the airport, he said. Flight delays averaged about 30 minutes, the FAA said.
The migration of diamondback terrapin turtles happens every year at Kennedy, which is built on the edge of Jamaica Bay and a federally protected park. In late June or early July the animals heave themselves out of the bay and head toward a beach to lay their eggs.
The peak of the turtle trouble usually lasts a few days, Marsico said.
Several pilots, some of them stifling chuckles, began reporting turtles on Runway 4L just as the morning rush hour was beginning at JFK, according to a radio recording posted on LiveATC.net.
"Be advised 30 feet into the takeoff roll, left side of the centerline, there's another turtle," called the pilot of American Airlines Flight 1009, a Boeing 767 that had just taken off bound for the Dominican Republic.
"There's another one on the runway?" asked the controller.
"Uh, well he WAS there," the pilot said as the big airliner climbed into the air.
American 663, a Boeing 737 headed to Fort Lauderdale, found its way to runway 4L blocked by three of the roving reptiles. After ground crews removed them, the plane taxied into takeoff position, received takeoff clearance -- and was promptly blocked by more turtles.
American and JetBlue, which has a hub at JFK, both said there were no major disruptions to their flights.
"We hope for faster animals next time," JetBlue said in a statement.
Female diamondback terrapins can grow up to 9 inches long and weigh up to three pounds.
Wayward wildlife is a serious concern at JFK and nearby LaGuardia Airport, which both sit on shorelines populated by geese, turtles, ducks, frogs and other animals. In January 2009 a U.S. Airways plane bound for Charlotte, N.C. was forced to land in the Hudson River after it hit a flock of birds and lost power in both engines. All 155 passengers and crew members were rescued.
In the past year, planes at JFK have collided with gulls, hawks, swans and an osprey, according to the FAA's database of wildlife strikes. In February, a superjumbo Airbus 380 flown by Emirates Airlines sucked an unidentified bird into one of its massive engines, causing about $30,000 worth of damage, the database shows.
"Other regions have their own issues with the runways, but this is kind of unique being so close to the water," FAA spokeswoman Arlene Salac said.
Road kill on runways can sometimes make them slippery, but there are no reports of turtles damaging a plane at JFK in recent years, the FAA database shows.
The main concern is for the turtles themselves, Marsico said. He said crews were loading the turtles into pickup trucks and giving them rides to the nesting beaches.
"We are trying to help wildlife out a bit here," Marsico said. "We built on the area where they were nesting for generations, so we feel incumbent to help them along the way."