Florida's self-defense law gives people wide latitude to use deadly force rather than retreat during a fight.
The shooting ignited racial tensions in this Orlando suburb. Civil rights groups have held rallies in Florida and New York, saying the shooting was unjustified. Late Wednesday, city commissioners in Sanford gave the police chief a "no confidence" vote.
"I must temporarily remove myself from the position as police chief for the city of Sanford. I do this in the hopes of restoring some semblance of calm to a city which has been in turmoil for several weeks," Lee said. "It is my hope that the investigation will move forward swiftly and appropriately through the justice system and that a final determination in this case is reached."
The police chief has said authorities were prohibited from making an arrest based on the facts and circumstances they had at the time of the shooting. He said he continued to stand behind his agency's investigation.
"As a former homicide investigator, a career law enforcement officer and a father, I am keenly aware of the emotions associated with this tragic death of a child. I'm also aware that my role as a leader of this agency has become a distraction from the investigation," Lee said.
It wasn't immediately how long the police chief would step aside.
The Justice Department and FBI have opened a civil rights investigation, and the local prosecutor has convened a grand jury April 10 to determine whether to charge Zimmerman.
Some people believe Lee should step down for good.
"If they wanted to diffuse a potential powder keg, he needed to resign," said pastor Eugene Walton, 58, who was born and raised in Sanford. "His inaction speaks loudly to the black community."
Also Thursday, the parents of Martin were meeting with U.S. Justice Department officials, hours before thousands of protesters were expected for a rally led by civil rights activist Al Sharpton.
Tracy Martin and Sybrina Fulton, who believe Zimmerman should have been arrested, were to discuss the police investigation into the shooting death of their son with Robert O'Neill, the U.S. Attorney for the Middle District of Florida, and Roy L. Austin Jr., who is deputy assistant attorney general of the department's Civil Rights Division.
Thousands of protesters were expected Thursday evening at an outdoor public park for a rally demanding that Zimmerman be charged. It had been scheduled to be held in a 400-seat church, but the rally was moved to accommodate the large number of protesters expected.
The rally is being headlined by Sharpton, who flew down to central Florida despite the death of his mother earlier in the day.
"My mom would have wanted me to," Sharpton wrote on Twitter.