The agency issued the order after an owl flew into the engine of a plane on the New York airport's tarmac last week.
On Dec. 7, JFK workers shot two snowy owls with a shotgun.
Birds can rarely bring down planes like they did in 2009 when a flock of geese disabled a commercial jet's engine and the pilot famously landed the plane in the Hudson River.
However, while they may not always be dangerous, bird strikes can be expensive for airports.
There were more than 1,300 wildlife strikes to civil aircraft in the U.S. in 2012, which cost airlines $149 million, according to an FAA report.
After the "Miracle on the Hudson," some 2,000 geese were rounded up around JFK and LaGuardia airports and euthanized in 2009.
Hundreds of birds have been killed near the airports since then, including swans, crows, starlings and Canada geese.
Since news of the recent snowy owl shootings broke, bird lovers have taken to social media demanding that the airport find a more humane way to deal with the animals.
Snowy owls are particularly beloved birds, thanks to the popularity of Hedwig, Harry Potter’s faithful feathered friend in J.K. Rowling’s best-selling book series.
But not all airports shoot owls that take up residence nearby.
Norman Smith of the Massachusetts Audubon Society has been catching and releasing snowy owls at Boston's Logan International Airport since 1981. He’s caught 20 in the area since November.
Although snowy owls are Arctic animals, they’ve been flying farther south in recent years due to population growth and dwindling food supplies.
The snow-white birds, which have a 5-foot wingspan, have recently been spotted as far south as the Carolinas.
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