By Agence France-Presse
Several dozen people are still missing and rescue workers, including police and troops, have been working to find survivors and victims as flood waters start to recede.
The toll is now the worst in a rain-related disaster for over three decades, and prompted Prime Minister Shinzo Abe on Monday to cancel a four-stop foreign trip planned for later this week.
The scale of the disaster is still becoming clear, with rescue workers only now starting to reach areas cut off by flooding or landslides.
Hundreds of people have been retrieved from rooftops where they sought shelter as flood waters rose.
The government said over 70,000 personnel including police, firefighters and troops have been deployed to look for survivors, or victims.
Abe is expected to visit the devastated areas later this week.