More than 200 flights were cancelled and dozens of train services suspended while many expressways were closed, the land ministry said, while 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 in Okinawa and other southern areas, emergency management authorities said.
Mekkhala was located about 90km south-southeast of Yakushima, moving east-northeast at roughly 30km/h, with sustained winds near 64km/h and gusts up to 90km/h, the Japan Meteorological Agency said.
Higos was about 260km southwest of Miyakejima Island, south of Tokyo, moving northeast at about 54km/h, with sustained winds near 83km/h near its centre and gusts up to 125km/h.
Mekkhala, downgraded from a typhoon to a tropical storm, passed 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.
"Last night the rain wasn't too bad. But this morning the rain didn't stop," said Chi, a dessert shop owner in northern Taiwan's Zhubei city.
"The road outside was flooded up to the knees, and inside our shop it was a little below knee level."
By Saturday, Mekkhala was expected to accelerate and approach western and eastern Japan, around the same time that Higos was forecast to draw close to the country's east, and possibly make landfall.
The combined impact of the storms and the rain front could boost rainfall across much of the country, it added.
More than 200 flights were cancelled on Friday at Naha Airport. The storm also began disrupting transport with warnings and suspensions affecting bullet train services in the Kanto, Tohoku and Shinetsu regions.
Typhoons are common in Japan during the summer and autumn.
with EFE
