Police ordered around 50 chanting demonstrators to disperse at about 4 AM and soon began removing tents and equipment while firefighters extinguished campfires.
Dump trucks carried away tents and supplies while crews removed makeshift barricades that had been blocking the street in front of the station and erected a high fence to keep people off the lawn and sidewalk.
"It was time," Mayor Betsy Hodges said at a news conference. "We have been balancing the safety needs of the precinct with the right for people to protest and have their voices be heard."
Police officers responding to a report of an assault in which Clark was a suspect said they arrived to find him interfering with paramedics who were trying to treat the victim. Police say a struggle followed and Clark was shot.
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Some community members have alleged that Clark was handcuffed when he was shot, but police dispute this. State and federal investigations are under way.
Protesters have demanded the release of any videos showing the shooting and called for a special prosecutor to be appointed instead of leaving it up to a grand jury to decide whether the officers should face charges.
Protesters won't be allowed to set up similar encampments or block streets for extended periods, the police chief said. It wasn't immediately clear when operations would return to normal at the station.
The new temporary fence blocked the sidewalk along the entire block and public access to the front door. A new fence across the street left the sidewalk open, a potential place for protesters to gather.
About 200 protesters and their supporters regrouped at 4 PM inside Minneapolis' City Hall, and speakers continued to press their demands for the release of videotapes and racial equity. The protesters then took to the streets, chanting and disrupting traffic in downtown Minneapolis.