"No chief minister in the last 63 years has made such remarks as made by Omar Abdullah, which are provocative and anti-national," said Jugal Kishore, BJP MLA.
Protesting MLAs were later evicted from the Assembly for disruptive behavior.
During the melee, a Panthers Party member and three BJP leaders-Jugal Kishore, Sukhnandan and Lal Chand-were injured.
The BJP Legislature Party is also expected to boycott the remaining part of the Assembly session, which ends on Saturday, Oct 9.
On Wednesday, Oct 6 Omar Abdullah said neither he nor his council of ministers were acting as puppets of the Centre.
"We are not puppets. We take decisions for our people and for their benefit," Abdullah asserted.