City Hall has been the site of conflict throughout the day. Authorities used an early-morning raid to break up an Occupy Wall Street encampment that had taken over a plaza outside the government headquarters for more than two weeks.
Police removed about 170 demonstrators who had been staying in the area overnight after being warned that such a camp was illegal and they faced arrest. City officials said 97 people were arrested in the morning raid.
Oakland police were backed up by deputies from 12 different agencies. No one was hurt.
The latest conflict came around 9:30 p.m. as some protesters began throwing rocks among a crowd that had reconvened at City Hall, where a haze of chemical smoke still hung in the air following a similar clash about an hour earlier only blocks away.
Helicopters scanned the area late Tuesday and scores of officers wearing helmets and carrying clubs patrolled the streets as protesters gathered only a few feet away.
City officials had originally been supportive of the protesters, with Oakland Mayor Jean Quan saying that sometimes "democracy is messy."
The city had warned the protesters that they were breaking the law and could not stay in the encampment overnight. They cited concerns about rats, fire hazards, public urination and acts of violence at the site.
The Oakland site was among numerous camps that have sprung up around the country, as protesters rally against what they see as corporate greed and a wide range of other economic issues.
The Associated Press contributed to this story.