The 26-year-old man and the woman checked into the lodge on Wednesday, police said.
On hearing the screams of the man on Thursday morning, people gathered and found him outside his room with blood stained clothes and he was rushed to a nearby hospital.
Later, he has been taken to a private hospital in Kozhikode where he is undergoing treatment, they said.
The woman has been taken into custody, police said.
Reports suggested the woman was in love with him.
However, he was planning to marry another woman.
In an act of taking revenge on the man, she allegedly cut off is genitals.