It happened on Caton Place near East 8th Street in Windsor Terrace around 9:45 p.m.
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The agent, whose name has not been released, was turning the corner when he came across a couple and their Belgian Shepherd.
The agent claims the dog charged at him, and he fired one shot, killing the animal.
"An off-duty Secret Service employee was involved in the shooting of an unrestrained and aggressive canine in Brooklyn, NY, this evening," the Secret Service said in a statement. "As this is an ongoing NYPD investigation, the Secret Service will not have further comment."
A Secret Service spokesman said the dog was wearing a leash but that no one was holding it when the animal charged the agent, but area residents who knew the dog raised doubts about the story.
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"The dog was definitely on a leash," one neighbor said. "It's a very friendly dog. He plays with our friend's dog sometimes."
Neighbors reported a heartbreaking scene with a sheet draped over the couple's beloved dog.
"That dog never did anything wrong," another neighbor said. "You don't go around shooting a dog."
Many said they were puzzled by the agent's extreme use of force.
"I just don't think it's acceptable for a professional, a trained professional, to use a firearm in that way," a neighbor said. "You'd think his first reaction would have been to kick or hit the dog."
The Secret Service agent went to Lutheran Hospital for evaluation.
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