The warrants were issued among others against BSP MP Qadir Rana, BJP MLAs Sangeet Som and Bhartendu Singh, BSP MLAs Noor Saleem and Maulana Jameel, Congress leader Saeeduzaman and BKU chief Naresh Tikait, police said.
They are wanted for violating prohibitory orders and provoking communal tension by making inflammatory speeches in different meetings (mahapanchayats) in the district, they said.
Action will be taken against them in two days time, Senior Superintendent of Police Praveen Kumar said.
A senior official said that ten police teams have been despatched to arrest those against whom warrants have been issued.
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The communal clashes in Muzaffarnagar and adjoining areas have claimed 47 lives and displaced over 40,000 people.
Meanwhile, under attack after two police officers reportedly admitted in a TV string operation having delayed action to contain Muzaffarnagar riots under "political pressure", Uttar Pradesh Minister Azam Khan said he has nothing to do with it and that he didn't want to give any clarification.
"And if I am found guilty, the channel should tell the punishment for me...I will accept the harshest of punishments, if found guilty....I am not that type of a person," Khan told reporters in Lucknow.