Banerjee said her decision was a protest against the violence unleashed by the Congress and the Left parties in the state during Wednesday's general strike.
Police vehicles were torched in Malda district, buses and motor-bikes damaged, and highways, crucial road junctions and railway tracks blockaded in the state during the nationwide one-day general strike called by 10 central trade unions including those affiliated to the Congress and the Left parties.
Accusing the Congress and the state's Left spearhead CPI-M of playing "dirty politics", Banerjee said she would continue her protests against the Citizenship Amendment Act (CAA), National Register of Citizens (NRC) and National Population Register (NPR) alone.
"I won't attend the meeting convened by Sonia Gandhi on January 13 as a protest against the Congress-Left hooliganism during Wednesday's strike," Banerjee said at the state Assembly.
"I'll continue my fight against the CAA, NRC, NPR, but I don't support violent protests and strikes," she said.
She alleged that the Congress and Left had "dual standards" and were trying to damage the state's economy by resorting to strikes.
"It is a cheap politics. We won't tolerate their double standards," said the Trinamool Congress chief.
Amid protests across the country, opposition parties will meet at Parliament annexe in New Delhi at 2 p.m. on January 13.
The Congress has sent invite to all like-minded parties to come together at a common platform.