Toyota had been aiming for a high February production plan to meet strong demand.
The automaker will reduce output again in November, but the impact will not be as painful as before and Toyota sees signs of recovery on the horizon.
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 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.
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 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.
Toyota could lose up to 480,000 units from January through March.