"As per the court order, a case has been lodged at Sadar police station against Mohd Azam Khan under section 124 (A) (sedition) on a written complaint filed by Bajrang Dal leader Ujjwal Gupta," Senior Superintendent of Police D K Chaudhary said.
A local court had on Tuesday directed the police to register the FIR and submit its report.
Chief Judicial Magistrate Pawan Pratap Singh passed the order on an application moved by Gupta on January 3.
At a public meeting on December 21 in Badaun, about 250 km from Lucknow, Khan had said Union Health Minister Ghulam Nabi Azad is the lone Muslim cabinet minister in the United Progressive Alliance government but he is a "Kashmiri".
"Only one Muslim minister s there in the cabinet and that too not of India, but from Kashmir. That Kashmir, which is still controversial and we don't know whether that is part of India or not," Khan had said.