A video, which recently went viral, purportedly showed Khatik inciting people to set a police station ablaze.
The video was shot on June 8 when Khatik, who represents Karera Assembly segment in Madhya Pradesh's Shivpuri district, was staging a protest at Karera Police Station against the killing of farmers in Mandsaur.
Karera's Sub-Divisional Officer of Police (SDOP) Anurag Sujania said the FIR was registered against Khatik, block Congress president Venus Goyal and others early today.
On June 8, Khatik was leading a protest march during which an effigy of Chief Minister Shivraj Singh Chouhan was burnt. The police poured water on the effigy in a bid to douse the flames, in which the woman legislator got partially drenched.
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This irked Khatik, who later sat on a protest at the police station along with her supporters and the video was shot during the sit-in.
The farmers' protest in Madhya Pradesh, which began on June 1, took a violent turn on June 6 when five cultivators were killed in police firing in Mandsaur district.
Subsequently, the farmers' protests witnessed bandh and arson as the agitation spread to other western Madhya Pradesh districts, including Neemuch, Dhar, Ratlam and Jhabua.
Chief Minister Shivraj Singh Chouhan had launched an indefinite fast in Bhopal on Saturday with an appeal for peace and met farmer leaders.
However, he ended his fast on Sunday saying peace has returned to the state. Before ending the fast, he assured people that those involved in the deaths of farmers in Mandsaur would be punished severely.