The protesters also hurled glass bottles at police personnel, and some of them were seen lifting tree logs to chase security forces away. Several people on both sides were reportedly injured.
The injured passengers are undergoing treatment at Uluberia Sub-divisional Hospital.
More than 240 people have been arrested and over 42 cases registered in connection with the violence since June 9, the police said.
Saumitra Khan alleged that the state government has "failed" to maintain law and order in the trouble-torn areas and "allowed the violence to spiral for vested political interests".
Any incident of violence, protest or attempts to block roads or hamper normal life will be dealt with "very strictly".
"I strongly seek that the accused leaders of BJP be arrested immediately so that the unity of the country is not disturbed and people at large do not face mental agony," Mamata tweeted.
The Howrah Municipal Corporation (Amendment) Bill, 2021, which proposes to separate Bally Municipality from the jurisdiction of the HMC, was passed by the state assembly last year.
Led by Brajrajnagar Citizen Committee and supported by clubs, civil groups, and members of political parties, the protest continued from 6 am till 8 pm.
Polling for the Howrah Dakshin constituency will be held on Saturday. BJP has fielded Rantideb Sengupta against TMC's Nandita Chowdhury and CPI(M)'s Sumitra Adhikari.