The Jaipur District judge's court charged the former minister under sections 376 (rape), 323 (causing hurt) and 506 (criminal intimidation) of the Indian Penal Code (IPC).
The matter was posted for next hearing to February 28.
Nagar, former Dairy and Civil Supplies Minister in the Gehlot government, was arrested by CBI in October last year after a married woman accused him of raping her.
The 35-year-old woman had alleged that Nagar raped and beat her up on September 11 last year after calling her to his official bungalow here on the pretext of getting her a job.