They include California Pacific Medical Center in San Francisco, Petaluma Valley Hospital and UCSF Medical Center.
Nine other hospitals in California were also fined, mostly for leaving objects inside patients after surgery.
CPMC was fined for two incidents, in which a surgical sponge and a retractor blade were left inside patients after surgery.
UCSF is contesting the penalty, which involved a small piece of drill bit that broke off during surgery and was left inside a patient.
At Petaluma Valley Hospital, a sponge was left inside a patient after surgery.