Detectives say scores of women responded to adverts seeking volunteers for “clinical research measuring blood pressure during sleep” over two years to November 2013.
They believe Hideyuki Noguchi, 54, gave the women sedatives after luring them to hotels and hot spring resorts.
Once the women were unconscious, he raped them and filmed each assault, police said.
Footage of the attacks was posted on the Internet or sold to producers of porn films, allegedly netting Noguchi more than 10 million yen ($85,000), TBS and other broadcasters said.
Noguchi is not know to have any medical training or expertise.
A spokesman for police in Chiba, east of Tokyo, said officers had confirmed at least 39 victims, aged from their teens to their 40s in Tokyo, Chiba, Osaka, Tochigi and Shizuoka.
Detectives believe they are just a fraction of the total number of women whom Noguchi attacked, thought to number well over 100, media reports said.