The department will provide the local police precinct councils three to five candidates that they will review.
The council will then provide feedback to the commissioner and the commissioner will make the final decision.
The local police precinct councils will also complete annual evaluations of commanding officers' performances.
"I think we've already seen some positive things come out of this reform process," Police Commissioner Dermot Shea said. "It helps build trust both ways."
Shea had served as a precinct commander at two NYPD precincts in the Bronx.
"You are like a miniature mayor of that command, the bonds to this day still exist," Shea said.
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