The factories near Bangalore are Toyota Motor's only vehicle plants in the world's sixth-biggest auto market, where the Japanese manufacturer generates just a sliver of global sales.
"A decision to suspend some of the members pending inquiry, for serious misconduct, was taken earlier in the week. This is in line with the company's rules and regulations," the company said in a statement.
It did not say how many workers were suspended.
On Sunday, Toyota Kirloskar Motor (TKM), the world's biggest car maker's Indian unit, said some workers had disrupted business as the management, labour union and local government negotiated wages.
The company and the factories' union are currently in discussions through meetings with the state's labour commission.
The company employs about 6,400 people.
The two plants have about 4,000 workers that belong to the union, union president Prasanna Kumar says.