The encampments were in San Diego's Civic Center Plaza and Children's Park.
However, in San Francisco, protesters were celebrating a rumored police raid that never came.
The San Diego Union-Tribune said an early caller to the newspaper said the San Diego protesters at the plaza were "surrounded with cops in riot gear with guns pointed at them."
The newspaper said police in riot gear with loud speakers moved against the crowd, which was mostly asleep, around 2:30 a.m. Videos showed dozens of officers with batons walking in a line.
Protester Robert Stanley, 63, a marketing consultant from Pacific Beach, told the newspaper about 150 officers moved into the plaza. "It looked like Napoleon's operation," he said. "Each position was taken up by a squad. It was like someone moving toy soldiers on a civil war front."
A protest leader said bail for those arrested was set at $2,500 each. A police spokeswoman said charges included illegal lodging, encroachment and curfew violation, but the Union-Tribune said most of the arrests were for obstruction and resisting arrest.
Occupy San Diego moved into the plaza Oct. 7, was ordered to leave but returned earlier this week.
Meanwhile, when a rumored police raid on Occupy San Francisco's camp on the south end of Justin Herman Plaza didn't occur it gave new life to the demonstration, the San Francisco Chronicle reported.
Earlier, when a rumor that a raid was impending, the camp was largely occupied by the homeless and a small core of activists.
When it was apparent by Thursday afternoon the raid wasn't coming, office workers, tourists and even a group resembling yoga instructors showed up at the site, the Chronicle said.
U.S. Rep. Barbara Lee, D-Calif., said Friday Oakland police overreacted to Occupy protesters and called for an investigation.
"These are peaceful protesters who have a right to petition their government," Lee said during an interview on MSNBC's "Morning Joe," The Hill reported. "The reaction was not appropriate."
Lee, who represents Oakland, said she's calling for an outside investigation into the response by police, who donned riot gear and reportedly fired teargas when protesters refused to leave an areas in front of Oakland City Hall Tuesday.
Scott Olsen, 24, a former U.S. Marine Corps corporal who served in Iraq, suffered a skull fracture Tuesday night after allegedly being struck by a tear gas canister, witnesses said. He was in fair condition Thursday in the intensive care unit at Highland Hospital, hospital spokesman Curt Olsen said, CNN reported.
Police say protesters had thrown objects at them, but even if that happened, Lee said, the police response was "inappropriate."
Lee said she has spoken with Oakland Mayor Jean Quan, who has apologized for violence that broke during the Occupy protest, and expressed support for the Occupy protests.
"I from day one have fully supported the Occupy movement. I think it's about time that people hit the streets and raise the concerns of the 99 percent," Lee said.