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SANFORD, Fla. — Several hours after the city manager announced that he had reached an agreement with Chief Bill R. Lee Jr. to resign over the Sanford Police Department’s handling of the Trayvon Martin case, the City Commission voted late Monday afternoon to reject Lee’s resignation.

Mayor Jeff Triplett was among the 3-2 majority of commissioners to vote “no confidence” in Lee last month, prompting him to temporarily step aside. But during a special meeting Monday to consider Lee’s future, Triplett was clearly conflicted amid a spirited debate punctuated with applause and standing ovations in the audience from backers of the chief.

In the end, Triplett voted in favor of Lee’s remaining in the department, once again as part of a 3-2 majority. He said he wanted to review the reports of an independent investigation about the Police Department’s handling of the case before making a decision.

“I am not ready to have him come back and run the Police Department,” Triplett said. “But I am not ready for this either.”

According to a copy of the agreement, Lee admitted no wrongdoing. In the three-page document, he explained that he was resigning at the suggestion of the city manager, Norton N. Bonaparte Jr., “solely to allow the city to move beyond recent events.”

The agreement said Lee would receive several lump-sum payments on May 4, including one equal to 98 1/4 days of pay and one for 217 hours of accrued leave. Bonaparte said in a brief interview Monday night that the agreement would have been worth $54,000 to Lee.

Lee stepped aside temporarily on March 22, after just 10 months in the job, amid local protests and a national uproar that raised questions about why Sanford police did not immediately arrest George Zimmerman, a neighborhood watch volunteer, after the Feb. 26 shooting and killing of Martin, an unarmed 17-year-old. Martin had been walking through a gated development where Zimmerman, 28 and Hispanic, lived and where Martin was staying as a guest.

Early Monday, Zimmerman, who was charged with murder by a special prosecutor, was released from jail on a $150,000 bond. His whereabouts remained a secret — he may be outside Florida — because of death threats, his lawyer said.

Before the commission voted, Bonaparte said that “the city has experienced great turmoil in the past two months” and that “we are hoping to stabilize the department and continue with this time of healing.”

With the Sanford City Commission rejecting the separation agreement, Bonaparte, who has been on the job only since September, said Lee would remain on administrative leave, and on the payroll, while the city conducts a national search for an interim police chief and pursues an independent investigation. In the meantime, Capt. Darren Scott, will remain the acting chief.