The Japan Meteorological Agency said "warm, moist air... was causing heavy rainfall with thunderstorms in western Japan" partly due to Kong-rey, which was downgraded to an extratropical low-pressure system from a typhoon.
The city of Matsuyama "issued the top-level warning, urging 189,552 residents in its 10 districts to evacuate and immediately secure safety", a city official told AFP.
While the evacuation was not mandatory, Japan's highest-level warning is typically issued when it is extremely likely that some kind of disaster has already occurred.
Forecasters warned that landslides and floods could affect western Japan on Saturday and eastern Japan on Sunday.
Due to rain, Shinkansen bullet trains were briefly suspended between Tokyo and southern Fukuoka region in the morning before resuming on a delayed schedule.
Kong-rey smashed into Taiwan on Thursday as one of the biggest storms to hit the island in decades.
It claimed at least three lives and injured 690 people, according to the National Fire Agency, which added a migrant worker death to the toll on Saturday.
The storm knocked out power to 957,061 households, 27,781 of which were still in the dark as of Saturday.
Scientists say human-driven climate change is intensifying the risk posed by heavy rains because a warmer atmosphere holds more water.
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