The crash occurred about 10 p.m. Wednesday as the passenger train, traveling an estimated 15 to 20 mph, struck the stationary Amtrak train, said Oakland Fire Department battalion chief Emon Usher.
Usher said the company told him that train went through a red light.
"According to the Amtrak representative, the train traveling should have never continued past the red signal," Usher told The Associated Press. "It's an equivalent to a red light," he said.
Most of the injuries were minor, but several people were taken to local hospitals, Usher said. Amtrak spokesman Cliff Cole said he could not comment on the report of the train running a red light.
He described the crash as it as a "low speed" collision between Amtrak's "San Joaquin," a train that operates between Bakersfield to Oakland, and the Coast Starlight, a train from Los Angeles to Seattle.
Francis Henrique, mother of a paralyzed passenger traveling on the train, said the impact "sounded like an explosion."
He said the wheels of each lead engine went off the track.
Authorities said there were injured on both trains, but there was no breakdown on how many from each.
About two hours after the crash, about 50 passengers were gathered inside the train terminal, talking to Amtrak officials, while Amtrak and local officials inspected the two trains.
There was no immediate word on what caused the crash, which is under investigation. Amtrak officials said train traffic has been temporarily suspended at the station.
Passengers who paid for travel on canceled trains can contact Amtrak to receive refund without fee or penalty, according to Amtrak.
The crash is the second significant incident in two weeks in the San Francisco East Bay area where there were injuries to Amtrak passengers.
On Sept. 30, 37 passengers and two crew members suffered minor to moderate injuries when an Amtrak passenger train collided with a truck at a crossing near Brentwood where there were no lights or gates.
The driver of the truck and a passenger inside were not hurt.