Automakers have already had to cut production because of difficulties finding semiconductors and other components as the pandemic disrupts manufacturing around the world.
The planned four-day halt to production at a Tsutsumi factory line, which makes Camry and Corolla models, will cut vehicle output by as many as 1,500 vehicles.
The latest January suspensions hit 19 lines at 11 plants in Japan, out of a total of 28 lines in 14 plants.
The Nissan Z car, a 400-hp, twin-turbo symbol of the struggling Japanese automaker's revival, is the latest product launch to be derailed by global supply chain woes.
The stoppages affect output of Lexus models and the Toyota Land Cruiser as the automaker runs short of components from plants in Southeast Asia where production has been disrupted.
The company says the persistent semiconductor shortage as well as uncertain geopolitical affairs have caused delays in logistics and parts delivery.
Toyota said heavy rains, especially in its home prefecture of Aichi in central Japan, impacted procurement of parts and will force it to stop production at a total of three lines in two domestic factories.
Toyota's global production plan for June stands at about 850,000 vehicles, a cut of about 100,000 vehicles.
Toyota cut its July global production plan by 50,000 vehicles.
Toyota said there was "a possibility" that it could lower its full-year production plan of 9.7 million vehicles as it faces a continuing shortage of parts due to the COVID-19 lockdowns in China.
VW brand, Audi and Seat will all cut production with the group's Wolfsburg plant in Germany restarting output with only one shift next week after the summer break.