The BJP MLA's wife Preeti Som was also booked in connection with the clash, while his PA, Chandrashekhar, is among 27 persons arrested in connection with the clashes, SSP Deepak Kumar said.
The clashes had broken out yesterday during the Mahapanchayat organised to protest slapping of National Security Act against Sangeet Som in connection with the Muzaffarnagar riots.
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The BJP MLA's wife Preeti Som, brother Sagar and PA are among 3,605 persons booked in connection with the clash in Khera village, Kumar said.
Four FIRs have been registered in connection with damaging government vehicles and vandalism during the clashes, he said.
The situation remained tense but peaceful, he said, adding that heavy police force has been deployed in the village after the clash to deal with any untoward incident.
Meanwhile, a lawyer was arrested in connection with the clash, which has triggered protests from advocates.
The agitating lawyers met Kumar to protest against the arrest and later went on strike. The SSP assured them that the matter would be probed.
At least 20 people, including RAF and police personnel, were injured and a number of government vehicles damaged in the clash.