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Neighborhood watch volunteer George Zimmerman faces murder charges in the 17-year-old's shooting death.
City commissioners in Sanford, Fla., voted 3-2 on Monday to reject the resignation of Police Chief Bill Lee over the Trayvon Martin shooting.
Lee submitted his resignation earlier in the day, a month after he stepped down temporarily amid the growing Trayvon Martin shooting controversy, the Orlando Sentinel reported.
During a special hearing, commissioner Randy Jones said Lee "needs to be reinstated immediately" and that most of the issues regarding the police department stem from a small number of people in Sanford, according to the Sentinel.
Commissioner Patty Mahany called Lee "one of the finest police officers in Florida," adding "This is not right. Just on a human level," according to the Sentinel.
Lee will now stay on administrative leave until an outside investigation is completed, which could be three to four months, USA Today reported.
More from GlobalPost: Trayvon Martin: Police chief steps aside over controversy
He temporarily stepped down last month in the wake of criticism over his department's handling of the investigation into the Feb. 26 shooting death of Martin, who was unarmed, according to CNN.
Earlier Monday, the man charged with second-degree murder in Martin's death, 28-year-old neighborhood watch captain George Zimmerman, was released from jail after posting $150,000 bail and pleaded not guilty to the charges, ABC News reported.
More from GlobalPost: George Zimmerman released on $150,000 bail (VIDEO)
According to investigators, Martin was walking back to the home of his father's fiancé on Feb. 26 when Zimmerman saw him, called 911 and began following him. Investigators said a fight broke out, but it's unclear who started it, ABC News reported.
Martin's death and the lack of an arrest in the case sparked protests nationwide. President Barack Obama even commented on the case, saying "If I had a son, he'd look like Trayvon."
More from GlobalPost: Obama speaks out on Trayvon Martin case (VIDEO)