He allegedly told his victims, many under 14 at the time, that what he was doing was a medical procedure, said the prosecutor's office in the city of Wels after several months' investigation.
It was only when one of the children complained about him that police arrested the doctor in January. News of his arrest led to a flood of accusations from other former alleged victims, with 95 so far identified.
The alleged offences date as far back as the early years of this century, say investigators.
The doctor's identity has not been revealed so as not to identify his alleged victims. According to Austrian press reports, he practised in a small, provincial town.
The doctor is set to go on trial later this year and if convicted faces up to 15 years in jail.