Violence broke out during the funeral procession of the Bajrang Dal activist on Monday who was killed in Karnataka's Shivamogga.
Vehicles were torched and police used tear gas to disperse crowds as right-wing groups protested against the murder of 23-year-old Harsha.
The victim, who worked as a tailor, was stabbed by unidentified persons on Sunday night.
Karnataka Home Minister Araga Jnanendra on Monday said the police have arrested three people in the murder case. He added that there are believed to be five accused in the case.
As the murder took place amid a raging controversy over hijab in the state, the police clarified that the murder hs no links with the row over hijab.
State Home Minister also said the probe so far has not revealed any link between the murder and the hijab controversy.
Meanwhile, a political slugfest has also broke out between the ruling BJP and the opposition Congress.
Karnataka's Rural Development minister KS Eshwarappa has blamed the "Muslim goons" for the murder. He also accused state Congress chief DK Shivakumar of instigating the killing with his comments during the hijab protests.
Responding to Eshwarappa's allegations, Shivakumar called him a "mad man" who should be sacked by the BJP.
The administration has imposed curbs on public gatherings and ordered that schools and colleges will stay shut.