The agency came under fire after published reports claimed it shot three birds over the weekend. Now the Port Authority says state conservation experts will trap and relocate the snowy owls instead.
In the last two weeks, five planes have been struck by the owls, which are migrating through the tri-state region.
An unusual number of snowy owls have been spotted in the northern U.S. this year and have been setting up winter residence at airports, fields and beaches far south of their normal range.
Bird strikes over New York have been getting special attention since 2009, when a flight successfully ditched in the Hudson River after hitting a flock of geese.