The case was filed in the court of Judicial Magistrate First Class Vinod Kumar Patidar who will record the statement of complainant Ajay Kumar Tiwari.
The complainant's advocate, Inderjeet Singh Bhatia, told reporters that his client has alleged that Khan made the comment on Kargil War for political objectives and divided India on communal lines.
The case has been filed under Section 124 (A) of the India Penal Code and other relevant sections.
The senior Samajwadi Party leader created a flutter by saying in Ghaziabad on Monday that "Muslims in the army" ensured India's victory in the Kargil War.
Image: Uttar Pradesh minister Azam Khan