Police fired teargas shells and used batons to disperse the crowd.
Protesters also burnt effigies of Banerjee and vowed to continue their fight for Gorkhaland.
Security personnel in large numbers were deployed in the hill district of West Bengal after widespread clashes between GJM activists and the police were witnessed on Saturday.
Around 2,000 Gorkha Muslims staged a protest march supporting the Gorkha Jamukti Morcha cause.
BJP MLA from Kaliagnaj Soumen Roy Saturday joined the ruling TMC, becoming the fourth saffron party legislator to do so since the West Bengal assembly poll results were declared in May.
The list, which is a mix of seasoned political players and greenhorns, has 17 women candidates, five more than the last elections, constituting roughly 41 per cent of the candidates.
The TMC, in total, bagged 75.02 per cent of the votes cast, whereas the BJP got some 14.48 per cent votes, in the four assembly segments.