Hideyuki Noguchi, 54, posed as a doctor and advertised for women from across Japan to take part in a medical study over a two-year time period, said to have ended in November 2013.
Police in Chiba, east of Tokyo say they have confirmed victims aged from their teens to mid-40s in several cities, including the capital.
Detectives say Noguchi lured the women to hotels and hot springs resorts where he gave them sedatives.
Once the women were unconscious, Noguchi would sexually assault and rape them, filming each assault, police said.
Footage of the attacks would be posted on the Internet or sold to producers of porn films, allegedly netting Noguchi more than 10 million yen (£56,543).
Noguchi is not know to have any medical training or expertise.
A spokesman for Chiba police said officers had confirmed at least 39 victims in Tokyo, Chiba, Osaka, Tochigi and Shizuoka.
However, they believe this is just a fraction of the total number of women whom Noguchi attacked, thought to number well over 100.