The 54-year-old man, an inmate of an ashram in Kollam, was rushed to the government medical college hospital here with critical injuries in the wee hours, police said today.
He underwent an emergency surgery and his condition is stable now, a hospital release said.
The woman in her complaint stated that the accused has been known to her family for the past few years and has been harassing her since she was a minor, police said.
He frequented her home for performing poojas and used to assault her during the visits, the complaint said.
When he tried to abuse her last night, she protested and chopped off his private organ with a knife, it added.
A senior police official told PTI that a case has been registered against the man under various sections of the Protection of Children from Sexual Offenses Act (POCSO) and IPC 376 (punishment for rape).
No case has been registered against the woman, he said.
The police declined to divulge details, saying the investigation is on.