More than 200 flights were cancelled and dozens of train services suspended while many expressways were closed, the land ministry said, while car maker Toyota briefly halted operations at a factory in the southern region of Kyushu.
Weather officials said a lingering seasonal rain front combined with warm, moist air from tropical storms Mekkhala and Higos brought downpours to wide swathes of Japan's west, threatening landslides, floods and swollen rivers.
About one million people faced evacuation orders after some were lifted for Okinawa and other southern areas, emergency management authorities said.
Mekkhala, downgraded from a typhoon to a tropical storm, was passing over the southern Ryukyu Islands on Friday after skirting Taiwan, where severe rains shut down parts of the island to keep about six million people from work or school.
Mekkhala was expected to accelerate and approach western and eastern Japan by Saturday, around the same time that Higos was forecast to draw close to eastern Japan, and possibly make landfall, the Japan Meteorological Agency said.
The combined impact of the storms and the stationary rain front could significantly increase rainfall across much of the country, it said.
Taiwan ordered offices and schools closed on Friday in its three hardest-hit southern regions of Kaohsiung, Pingtung and Tainan, where severe flooding shut down a section of the island's main north-south railway link.
In the northern city of Hsinchu, home to the world's largest contract chipmaker, TSMC, offices and schools closed from noon.
In a statement, TSMC said its factories were operating as normal, and its Taiwan facilities had prepared for the rain.
About six million people live in the four affected areas of Taiwan.
In parts of largely rural Pingtung, almost a metre of rain has fallen since Thursday.
No casualties have been reported in Taiwan but authorities in Hualien county were evacuating nearly 200 residents from two townships downstream of a rapidly filling barrier lake in the mountains.
Barrier lakes result when rocks, landslides or other natural blockages form a dam across a river, usually in a valley, holding back flows or even natural drainage.
In 2025, 19 people died in another part of Hualien when another barrier lake breached its banks during Super Typhoon Ragasa, unleashing a wall of water and mud into homes.
Rain is not all bad news for southern Taiwan, which relies on the traditional summer and autumn typhoon season to fill its reservoirs after winters that are typically dry.
