The actor is said to have violated the Indecent Representation of Women (Prohibition) Act 1986, after appearing with inappropriately dressed dancers to perform the track 'Chamak Challo'.
The case was issued against the Ra.One star following a performance of the popular film song at the inauguration of a textile showroom in Ernakulam, reportsThe Times of India.
The star earlier spoke out about media-created controversies surrounding his film prior to its release in October.
The actor's portrayal of a Tamil speaking character in the project had also caused upset amongst film audiences in the south of India.
Khan's new project Don 2 releases on Friday.