The man was being arrested for an unsolved murder when he began fighting with officers, according to police.
During the struggle, one of the officer's weapons discharged, striking the suspect in the leg, police say.
The shooting occurred in East New York near Liberty and Georgia Avenue just before 12 p.m.
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The man was taken to a local hospital in stable condition. He was wanted for questioning in an unsolved manslaughter in Brooklyn, but no charges have been filed.
None of the officers were hurt in the scuffle, but one officer was evaluated for tinnitus, or ringing of the ears.
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