Flights were cancelled, bullet trains partially suspended and factories shuttered on Tuesday as Typhoon Khanun headed past Japan's southernmost main island of Kyushu, bringing heavy rain.
The typhoon last week reportedly killed at least two people, injured more than 100 and cut off power for several hundred thousand people in the southern Okinawa region before barrelling towards Taiwan.
The weather system then swung back to the Okinawa area and on Wednesday was due to roar along the western coast of Kyushu towards South Korea, according to forecasters.
Japan Airlines on Tuesday cancelled 132 flights, which affected some 8,390 people, a spokeswoman told AFP.
ANA also scrapped flights between Kagoshima in southern Kyushu and Tokyo.
The country's "shinkansen" bullet train was suspended in part of its southern route, while many other local commuter and express trains were cancelled, Kyushu Railway said in a statement.
"Please be vigilant about landslides, floods in low lands, and increase and spillover of water in rivers, storms and high waves" at seas, Japan's weather agency warned local residents on its website.
Kagoshima prefecture issued non-compulsory evacuation orders to about 540,000 residents, setting up 314 shelters, officials said.
Other regions north of Kyushu were also bracing for the violent weather system, with carmaker Mazda announcing its factories in Hiroshima and Yamaguchi would suspend operations on Wednesday and Thursday.
The storm forced Nagasaki, one of the main cities on Kyushu, to move indoors and scale down its annual commemoration ceremony of the 1945 atomic bombing scheduled for Wednesday.
In South Korea, the approaching weather system prompted the evacuation of tens of thousands of people at the World Scout Jamboree.