Chief Judicial Magistrate, Srinagar, Rajiv Gupta issued the arrest warrant against Khan, an MLA from Rajouri, following an application moved by police.
Yesterday, police had registered a case against Khan after a lady doctor, wife of a separatist leader, alleged the minister had called her to his office in the Civil Secretariat last month and attempted to molest her.
Official sources said a police team had been constituted to arrest the former minister.
The sources said the police had summoned Khan to present himself for investigations today and moved the court for an arrest warrant after he failed to appear.
Khan had yesterday moved an application for anticipatory bail in the Jammu wing of the state High Court but it was rejected.