Port Authority officials did not “run afoul” of federal law when they executed three snowy owls considered a threat to aviation at Kennedy Airport in 2013, a Manhattan federal appeals court decided Tuesday.

Ruling in a suit by the group Friends of Animals, the Second U.S. Circuit Court of Appeals said the U.S. Fish and Wildlife Service had authority to give the Port Authority a broad “depredation permit” allowing the emergency “take” of any species putting planes at risk.

“It is clear in context that, as used in the . . . permit’s emergency-take provision, the term contemplates (and thus implicitly authorizes) the use of lethal methods,” the court said.

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The lawsuit was filed after disclosures that the Port Authority was shotgunning the owls as part of an extermination program. Amid controversy, officials said five planes at area airports had been struck by owls, but agreed to begin trapping instead of killing them.

Michael Harris, a lawyer for Friends of Animals, said the adoption of a nonlethal policy on the owls was one positive result of the publicity and the lawsuit, but complained that the Second Circuit ruling highlighted the absence of humane protections in federal law.

“What the Court of Appeals has actually affirmed is that our nation’s laws, as currently constituted, legitimizes the indiscriminate, unnecessary killing of animals,” he said. “When birds that pose little to no risk to air safety can be lawfully murdered, like those three snowy owls, it speaks loudly to the nature of a nation’s moral character.”

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The Port Authority did not return a call for comment. In 2013, it said snowy owls had begun migrating to the New York area in higher than typical numbers, but pledged to strike a “balance” between “humanely controlling” birds and safeguarding passengers.

The court, in its ruling, noted that birds were no laughing matter for aviation. Among other episodes, it cited the 2009 incident in which a jetliner had to land in the Hudson River shortly after leaving LaGuardia Airport when it collided with a flock of geese.