Dr. Yashwant Giri, a 58-year-old anesthesiologist, is suspected of assaulting them while they were undergoing surgery at Placentia-Linda Hospital in Placentia.
The most recent case involved a 36-year-old patient in March, authorities said.
"These acts occurred when the patients themselves were under anesthesia, so the victims themselves aren't going to know it," said Placentia Police Det. Corinne Loomis.
In a statement, a hospital official said: "We take allegations such as this very seriously. The hospital and medical staff immediately launched an internal review. The physician resigned from our staff last month. We have reported the incidents to California Department of Public Health, the medical board and local authorities, and we are cooperating fully with their investigations."
Giri's resignation came after the second alleged incident. The first one involving the teenager was never reported to police in 2009.
Police said hospital workers in the operating room at the time reported the abuse.
"The investigation that the hospital says they did in 2009 in their opinion was inconclusive," Loomis said. "The doctor denied the allegations and they didn't believe they had enough to substantiate, so they concluded there wasn't anything more to do with it."
Police said there may be other victims. Authorities say Giri worked at West Anaheim Medical Center, Anaheim Regional Medical Center, and Western Medical Center-Anaheim.
Giri remains in custody with bail set at $100,000.