The two counts - felony sexual battery and felony sexual penetration with a foreign object - were filed Monday against Dr. Yashwant Giri on behalf of a 28-year-old woman.
The woman told police that Giri, 58, sexually assaulted her before she went into surgery at Placentia-Linda Hospital in April 2010.
She decided to come forward last week after encouragement from her family and therapist, officials said.
Giri was arrested last May. He is out of custody after posting $1 million bail. He's accused of sexually assaulting a 36-year-old woman while she was under anesthesia during surgery.
In a statement, a Placentia-Linda Hospital official said, "The hospital takes these allegations very seriously. We immediately launched an internal review in March, 2011, following an employee reporting to the hospital that they witnessed inappropriate behavior by this physician. Based on our internal review, we called the police, the California Department of Public Health, the medical board and local authorities, and we have fully cooperated with their investigations."
But authorities allege that at least one earlier case in 2009, which involved a 16-year-old girl, was never reported by the hospital to police.
The same year, a 45-year-old patient at Gardena Memorial Hospital accused Giri of sexual assault. He denied it. Police said the case went cold until the Orange County allegations emerged.
So far, the district attorney has charged Giri in three cases. Three other women have also accused the doctor of sexual abuse.
Giri would not comment on the charges. He has pleaded not guilty. His next court appearance was scheduled for Nov. 14.
Giri's medical license has been suspended, pending the outcome of the investigation.
Police are concerned there may be other victims. Anyone with information was asked to contact police at (714) 993-8194.