Protesters stopped at City Hall, where a city councilman addressed the crowd and said he will ask for an investigation into police response to the protests over the weekend, when the latest wave of protests started.
Bay Area Rapid Transit officials said the station in downtown Berkeley was closed as a precaution. A City Council meeting scheduled for Tuesday night was canceled after threats to disrupt it, said Berkeley Mayor Tom Bates.
Amtrak passenger train service was suspended between the Oakland Coliseum station stop and Richmond because of the protest, officials said.
The agency arrested 223 people Monday on suspicion of resisting arrest, obstructing police and other charges, said Ernie Sanchez, assistant chief of the CHP's Golden Gate Division. Berkeley police arrested another nine people.
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Sanchez told the San Francisco Chronicle the agency will also ask the Alameda County district attorney's office to increase bails and charges.
Those arrested face bails of up to $50,000, and many remain in custody, he added.
A woman stuck in traffic went into labor during the protest, but fire crews were able to get her to a hospital, KPIX-TV reported.
"The CHP respects the public's right to gather and demonstrate, but it needs to be done in a safe manner," Sanchez said. "At this point, they've made their statement and we respect that. Now, we're asking them to stop."