The protestors raised slogans against the state government, saying the murder was the result of its "anti- Hindu" policy.
VHP leader M B Puranik said the state government was supporting only minority communities.
"Terrorists" had hijacked the government and they were trying to eliminate Hindus, he alleged, addressing protesters.
The police stopped the protest and took into custody local leaders, including Jagadish Shenava, M B Puranik, Sharan Pumpwell and hundreds of other VHP and Bajrang Dal activists.
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At Udupi also, workers of BJP and Bajrang Dal staged a road roko at Triveni circle to register their protest against the killing of Rao.
Addressing the protesters, former MLA K Raghupati Bhat alleged that the law and order situation in the state had collapsed.
A well-hatched conspiracy to murder Hindu activists was going on in the state, he alleged.
Police, which maintained tight vigil at the spot of the agitation, took into custody the participants.They were taken in a vehicle and released later.
State BJP secretary Yashpal Suvarna, Bajrang Dal convener Dinesh Mendon, Vishwa Hindu Parishad (VHP) city unit president Santosh Kumar Bolje and activists of different pro-Hindu outfits took part in the protest.
All the four were arrested within hours of the attack.
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