The three-day suspension is likely to mean a production fall of 3,500 vehicles.
The automaker has asked suppliers to make up for lost output so it can build an additional 97,000 vehicles between December and the end of March, Reuters reported.
The comment comes after the automaker said a parts shortages would cost it 14,000 vehicles in lost production in December.
The latest stoppages will bring lost output to 9,000 vehicles, the automaker said, and affect production of Lexus models and the Land Cruiser.
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 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 said it will work with minivehicle specialists Daihatsu and Suzuki to develop small electric commercial vans.
Toyota President Akio Toyoda told union members in Japan that suppliers would be exhausted unless there was a "sound" production plan.
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.