Modi's Hindu nationalist Bharatiya Janata Party (BJP) and the Trinamool Congress -- which runs West Bengal state -- have accused each other of instigating weeks of violence during and since India's recent election.
Police fired tear gas and water cannon to disperse more than 20,000 BJP demonstrators as they attempted to march to police headquarters in Kolkata, the state capital.
The BJP supporters waved party flags and chanted Hindu slogans as they went through the cramped streets of the British colonial-era city.
Police used batons to clear protesters blocking an arterial road near their headquarters and arrested six women supporters trying to sneak into the building.
"We want an end to the Trinamool Congress misrule in West Bengal," one shouted before being arrested.
The latest protest comes a day after police said three political activists had been killed since the weekend -- including two BJP members whose bodies were found hanging from a tree.
A Trinamool member was killed in a bomb attack late Monday.
Both parities have accused each other of the violence.
The BJP, which has traditionally held sway in the Hindi-speaking belt in the north, has been trying hard to pick up support in West Bengal.
In the elections that ended last month with a big national victory for Modi, the BJP increased its tally of seats in the state to 18 from just two at the last vote in 2014.