The dog, a Belgian Malinois named Billy, did not respond when its handler ordered it to release the other officer, the San Francisco Chronicle reported.
Police had responded to a report of a burglary in progress at the Coast Guard Recruiting Center in Alameda just after 6 a.m. PST. Douglas Wayne Kirk, 56, who appeared just after the shooting, was arrested and charged with burglary.
The Alameda Police Department is investigating the shooting. The officer who was bitten was treated at an Oakland hospital.
Billy had been an Alameda police dog for three years and began working with its current handler in September.