Mayor Jim Kenney condemned the actions.
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"We tolerated it last night for too long and that was a mistake. We will not tolerate it moving forward," he said.
Philadelphia Police Commissioner Danielle Outlaw echoed the mayor.
"While every person has a right to defend themselves and protect their property, we do not endorse or condone any form of vigilante justice," she said.
Just after 4 a.m. Tuesday morning, a South Philadelphia gun shop owner opened fire on four alleged intruders. One of the intruders was killed, and another was injured after they allegedly cut the chain link fence and entered his business.
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Kenney said he was troubled by the loss of life.
"While I respect the rights of individuals to protect their property, I am also deeply troubled about the ease another life was taken amidst the chaos," he said.
High profile defense attorney, Fred Perri, says Pennsylvania has what's known as the Castle Doctrine. It is a modified stand your ground law. It applies to certain circumstances and allows people to use force to protect themselves.
"Gives homeowners, storeowners, people in their cars the right to use deadly force if they perceive that force being used on them and there's not duty to retreat," he said.
Police on scene of the alleged gun shop break in on the 1500 block of Front Street told Action News at least one intruder may have been armed with a gun. But Outlaw stopped short of confirming that at a press conference.
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As more home and business owners take matters into their own hands, city leaders are trying to minimize bloodshed.
"We strongly encourage if there is a non-violent way to protect one's self or property that should be the option," Outlaw said.
No charges have been filed in the shooting at the gun shop.
The investigation is ongoing and the owner is cooperating with authorities. The owner has had no comment.