Heavy rains had already left a group of 18 people stranded at the banks of a swelling river. They were evacuated to higher ground to be rescued.
Japan has been hit by heavy rain as the country braces for a severe tropical storm with hundreds of flights cancelled and large areas evacuated.
Storm Krosa is expected to make landfall Thursday afternoon on the southern island of Shikoku.
More than 400,000 people have been evacuated from the region while many trains were halted and highways closed.
Almost 700 flights have been cancelled, affecting travel during the summer holiday season.
Krosa is classified as a tropical storm, one notch below the typhoon category.
After landfall it is expected to move north toward the Sea of Japan.
Heavy rains had already left a group of 18 people stranded at the banks of a swelling river. They were evacuated to higher ground to be rescued.
Japan’s weather agency said the storm had weakened from the previous days but still warned of potential record rainfall, mudslides and floods in the affected areas of the Pacific coast.
The travel disruptions are thought to affect millions of people who are visiting their hometowns for the Bon holiday when Japanese people traditionally pay respect to their ancestors.
According to Japanese media, the train cancellations affect connections on Shikoku itself but also many of the Shinkansen bullet trains between Tokyo, Osaka, Hiroshima and the south-western province of Fukuoka.
Ferries to Shikoku have also been cancelled as high waves lashed the coast.
Japan on Thursday is also marking the anniversary of its surrender in World War Two and several memorial services in the affected regions had to be cancelled, British Broadcasting Corporation reports.