In his letter to Patil, Azmi alleged that Bhagwat's remarks are meant to communally polarise the atmosphere ahead of Assembly polls in the state, due in October.
"Our constitution is secular and to call all Indians as Hindus is a conspiracy to deny freedom of religion to minorities. It is a veiled threat meant to convert people who practice other religions," Azmi said in a letter.
The RSS chief had on Sunday said that India is a Hindu nation and Hindutva is its identity, sparking a major controversy.
"This highly dangerous, volatile, divisive and controversial rhetoric by Bhagwat must be taken as an offence meant to create disharmony among different communities of the country. The statements made by Bhagwat are punishable under sections 153 (A), 153 (B), 500, 505 and 295 of the IPC," Azmi said in the letter.
He alleged that Bhagwat was trying to polarise the atmosphere in Maharashtra ahead of the Assembly elections due later this year.
"These statements made by Bhagwat, that have hurt the religious sentiments of minorities are a part of a conspiracy to polarise (the atmosphere) during the elections. The RSS and its related outfits are making such statements frequently since the BJP government came to power at the Centre," he added.
"I request Home Minister to direct the state police to lodge an FIR against Bhagwat to discourage communal minded people from doing unconstitutional activities," Azmi said.