The incident came to light on Friday when the police received a complaint from the jail authorities.
The victim was taken to a hospital where doctors confirmed the sexual assault and a case under Section 377 of IPC (Unnatural offences) was registered at Samaypur Badli police station, a senior police official said.
In his complaint to the jail authorities, the victim also alleged that a warder in the prison had set the accused, a 29-year-old man, to sexually assault him and to threat other inmates in the prison premises.