Ishu Pawar was caught in the act by his neighbours yesterday when his wife was away for some work, they said.
The neighbours intervened when they heard screams of the child, police said, adding they informed Pawar's wife about the incident when she returned home.
In her FIR with police, the complainant alleged that Pawar had on earlier occasions also raped the girl and threatened her of dire consequences if she revealed about the alleged incidents.
Pawar has been booked under sections 376 (punishment for rape) and 506 (punishment for criminal intimidation) of the Indian Penal Code (IPC).
