The suspension will be extended to one more facility from Tuesday evening, meaning all of the automaker's domestic factories have been affected.
Company officials said a timeline has not been set for the resumption of operations.
Toyota said a malfunction in the production system has made it impossible to order components. Officials said the company will decide by Tuesday evening how it will proceed in the coming days.
Toyota halted domestic plant operations last year
Toyota was forced to stop operations at all of its domestic plants in March of last year after one of its suppliers was targeted by a cyberattack.
But company officials said that as of now, they do not believe the current issue was caused by a similar attack.
Toyota business partner awaits information
Fewer people than usual were visible around Toyota's Motomachi Plant in Toyota City, Aichi Prefecture.
An employee who emerged from the factory shortly before 11:00 a.m. on his way home said he had arrived at work around 6:00 a.m. He said his boss told him, "the line won't move today." The employee said he does not know anything about the cause of the stoppage, but he wants the plant to resume operations as soon as possible.
A man working for one of Toyota's business partners who visited the factory on Tuesday said that Toyota informed him of the suspension on Monday night. He also said that he is waiting for more information from the company.
Industry ministry will do 'whatever it can'
Japan's Economy, Trade and Industry Minister Nishimura Yasutoshi said at a press conference on Tuesday that Toyota is working to identify the cause of the problem.
Nishimura added that the ministry intends to gain a full understanding of the issue and "do whatever it can" to help the situation.