An OES alert said the 6-foot surge wave at Crescent City came in at around 30 mph.
Debbie McAndrews of the Crescent City Harbor District said two docks were torn apart and numerous boats were knocked loose.
"We couldn't see waves," McAndrews said. "The water looked like you were watching a rolling river."
Harbormaster Richard Young said that there were no injuries and no boats had sunk, but that major damage had occurred to at least three docks.
"We're trying to look on the bright side," Young said. He added that the dock damage could run as high as $700,000.
Warnings and tsunami watches were issued in Japan, Russia, Hawaii Alaska, British Columbia, Washington, Oregon and Northern California, but were later withdrawn. Surge waves were forecast to continue until 6 p.m. or a little later along the California coast.
A series of small waves none measuring higher than 16 inches hit Japan's coast, coming in well under initial predictions.
At the Eureka office of the National Weather Service, meteorologist Troy Nicolini said the wave height was underforecast, a product of the complexities of determining how a tsunami will act when it encounters a shoreline.
"Crescent City amplifies the wave height," he said.
The city is familiar with the power of ocean surges.
A 1964 tsunami washed away 11 people the only tsunami to take lives in the continental United States.
Surge waves were reported Wednesday as far south as Port San Luis in San Luis Obispo County, according to a "special weather statement" from the National Weather Service.
San Mateo County Sheriff's Office of Emergency Services and Homeland Security Director Lt. John Quinlan said he had been in direct contact with the weather service. Quinlan described a surge wave as being "way below a category of a tsunami.
"It was so far below the threshold, there were no warnings given," Quinlan said. "It's a 6-foot surge, which happens all the time. It's a rogue wave."
Quinlan said he was in contact with the San Mateo County Sheriff's Office, as well as the Pacifica and Half Moon Bay police departments and the California Department of Forestry and Fire Protection.
He said his biggest concern locally was the ocean's undertow, which may prove dangerous for swimmers and surfers.
"My biggest concern is the undertow," he said. "They kill people every year. It's very strong. The weather service warned us about that."
Eureka Times-Standard reporters Kim Wear, James Faulk and Chris Durant and wire services contributed to this report.