The City Council rejected the resignation by a vote of 3-2 and called for Bill Lee Jr.'s immediate reinstatement, the Orlando (Fla.) Sentinel reported.
City Commissioner Patty Mahany said Lee submitted his resignation during the weekend. He had temporarily removed himself last month amid complaints about how his department handled the investigation of the Feb. 26 shooting of 17-year-old Trayvon Martin by neighborhood watch volunteer George Zimmerman, the Los Angeles Times said.
"Elected officials used this man as a scapegoat to heal our community," Mahany told the Times in a telephone interview. "Our community was never broken."
She said she blamed activists whose protests "ruined the reputation and career of a really stellar law enforcement officer."
Lee "is nothing but a scapegoat," Mahany said. "Our police department did nothing wrong."
Martin was shot to death Feb. 26 as he was walking through a gated community in Sanford. Zimmerman, 28, told police he shot the teenager in self-defense. He was taken to the police station that night and was released after police accepted his self-defense argument.
Against a backdrop of growing outrage and nationwide demonstrations, Florida Gov. Rick Scott appointed a special prosecutor in the case. She eventually charged Zimmerman with second-degree murder. Zimmerman, whose father is white and mother is Hispanic, was taken into custody April 11. He was released early Monday after posting a $150,000 bond. His movements will be tracked by an electronic monitoring device.
Also Monday, Zimmerman's attorney apologized for the timing of his client's apology to the victim's family. Mark O'Mara said he didn't realize Martin's family would think the apology came at a poor time, CBS News reported.
"Had I known or been told that that wasn't the time, it wouldn't have happened. So, I apologize for that," O'Mara said.
During his bond hearing last week, Zimmerman addressed Martin's family, saying he was sorry for the loss of their son.
Zimmerman had apparently asked if he could apologize privately but Martin's parents rejected that suggestion at a news conference, the report said.
"He had a Web page -- never apologized there. Had the voice mails we've heard -- never apologized then," the family's attorney, Benjamin Crump, said. "So, we feel that you all can conclude for yourselves what motivations there are."
O'Mara said Zimmerman wouldn't have apologized at the hearing had he seen the news conference.
After the bond hearing, the Martin family's attorney said Zimmerman's apology appeared "insincere."
O'Mara said he remained concerned for Zimmerman's safety, even though he hasn't received any serious threats recently, MSNBC.com said. He said he was maintaining contact with law enforcement officials.