The arrest was opposed by some religious and political outfits, following which security has been beefed up in sensitive areas here, SP (City) Om Prakash said.
Dungar was arrested for allegedly instigating the violence by making inflammatory speeches during the Mahapanchayat meet organised to protest slapping of NSA on Som in connection with Muzaffarnagar riots, he said.
The Bajrang Dal leader was absconding since the incident and was arrested from Kankar Khera region, the SP said.
The Mahapanchayat was called in September by Som's brother Sagar and wife against slapping of the National Security Act on the MLA in connection with the Muzaffarnagar violence.
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Clashes broke out when rumours spread that some women were injured in caning by police at the venue. Irate villagers had pelted stones on the police personnel deployed there and burnt police vehicles.
Following the incident, a case was registered against Dungar, 130 named accused and 3,500 unidentified accused.
62 persons were killed and over 40,000 rendered homeless by the riots in Muzaffarnagar and adjoining areas.