Police said they resorted to "mild" lathichargeand used tear gas to disperse the agitators as a section of them pelted stones at the forces, damaged vehicles and burnt tyres during a protest called by the BJP and others in Sirsi.
The saffron party has maintained that 18-year old Paresh Kamalakar Mesta was a "Hindu activist" killed by "Jehadi elements", and demanded a probe by the National Investigation Agency (NIA).
Mesta's family and locals have alleged that he was abducted andkilled amid reports that the body bore marks of attack bysharp objects.
Police, however, rejected these claims, citing the postmortem report.
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Karnataka Chief Minister Siddaramaiah has accused the BJP of using the incident for "political gains".
Senior police and district administration officialssaid the situation at Sirsi was now under control and peace had been restored by dispersing the crowd.
Police said the situation in Kumta was also normal.
BJP and some other outfits had called the protest in Sirsi, demanding the arrest of those responsible forMesta's death.
Meanwhile, a political slug fest has erupted betweenthe ruling Congress and the BJP, as the two hold each other responsible for theincident.
"A desperate @BJP4Karnataka stoops so low as to usethe unfortunate death of a youth Paresh Mesta in Honnavar for political gains...People aregetting hurt by their irresponsible acts," Siddaramaiah said in a tweet.
Home Minister Ramalinga Reddy claimed such incidents wereprovoked "purposefully" by the BJP, keeping in mind the assembly elections, due early next year.
The BJP, which has termed the death as "the handiwork of jehadi elements", today petitioned Governor Vajubhai Vaila, demanding a probe by the NIA in the case.
BJP leaders led by K S Eshwarappa staged a protest march from Vidhana Soudha, state secretariat, to Raj Bhavan here.
Calling Mesta a "Hindu activist", Eshwarappa accused the government of turning Karnataka into Kerala, and claimed this was20th such killing of a Hindu activist in the state.
He alleged police and doctors (involved in postmortem) had been "utilised" by the government to "close the case".
Meanwhile, the Karnataka Pradesh Congress Party (KPCC) accused the BJP of playing "politics of cadaver".
"We do not discriminate. Whether a Muslim, a Hindu, a Christian or a Parsi is killed, it is deplorable. Nobody can support it. But the BJP loves doing the 'politics of cadaver'. It incites communal tension in the state for political gain," KPCC working president Dinesh Gundu Rao alleged.
Talking to reporters, he rubbished the accusations made by BJP leaders thatthe Congress-led state government had failed to containmurderous assaults on RSS workers.