As per the police, Kothari had uploaded a picture on Twitter with the caption, "Scindia taking Kamal Nath for immersion", the police said.
The case was registered after Congress Secretary Rakesh Yadav lodged a complaint against Kothari in Vijay Nagar police station on Monday.
Yadav, in his complaint, said: "Bharatiya Janata Yuva Morcha's national Vice President and party's state spokesman Rahul Kothari has made a derogatory comment in his tweet".
Reacting to the complaint, Kothari tweeted: "The case against me by the Congress is an evidence of undeclared emergency in the state".
Feared from the main opposition party in the state, the state government is imposing fine over protest and filing complaints. But the state government cannot stop the BJP's struggle for people. The Chief Minister who has no respect then what is the point of insult! We won't bow or stop before a puppet, tweeted Kothari.