The IGP was not in the car when it was set on fire, they said.
Paresh Kamalakar Mesta (18) had gone missing on December 6. His body was found near a lake in Honnavar in that district on the night of December 8 under mysterious circumstances, leading to a tense situation.
Police said the crowd turned violent today and pelted stones at them and their vehicles, injuring some of them.
"The situation is now peaceful and nder control. We are questioning some people in connection with the incident," Uttara Kannada Superintendent of Police, Patil Vinayak Vasantarao told PTI.
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Police however rejected these claims, citing the post-mortem report.
BJP and some other outfits had called for protest in the district today, demanding the arrest of those responsible for Mestas death.
The party had yesterday demanded a probe by the National Investigating Agency (NIA) into the killing.
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