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The complaint was filed against Raut, who is the executive editor of the paper, by BJP Yavatmal convener Nitin Bhutada, he said.
As per the complaint, Bhutada claimed Raut had written an objectionable article against PM Modi on December 11.
A case was registered against Raut under Indian Penal Code sections 153 (A), 505 (2) and 124 (A) at Umarkhed police station for promoting enmity between different groups and other offences, the official said.