More than 5.2 million people have been issued evacuation notices across the country, authorities said.
Madoka Kubo, who runs a hotel in historic city of Hitoyoshi in Kumamoto prefecture, told Reuters that all reservations had been cancelled and her hotel was now being used to house elderly people who had been evacuated from nearby areas.
Airlines, including ANA Holdings and Japan Airlines , have already announced cancellations of nearly 800 flights. Train services have been suspended in many areas of Kyushu while hundreds of bus and ferry services have also been halted, according to the transport ministry.
Typhoon Shanshan is the latest harsh weather system to hit Japan, following Typhoon Ampil, which also led to blackouts and evacuations, earlier this month.