The dead man was found drowned in a river in Niigata province shortly after his car was dragged from the water.
Four other people, including a 93-year-old woman, are reported missing in the province.
Niigata and Fukushima , mountainous regions which were badly hit by March’s earthquake, tsunami and nuclear accident, are the worst affected by flooding.
A 63-year-old man is reported missing in Fukushima, where 40 people were rescued Saturday after spending the night in cars or buses trapped by water of mud.
The country’s defence forces have been called out for the search and rescue effort.
Despite a maximum alert from forecasters, nobody had been ordered to leave their home on Saturday, although 400,000 were advised to do so.
Earlier floods killed at least 59 people in South Korea and the defence ministry said that landmines from North Korea had washed up across the border.
Heavy rainfall has also hit Indonesia, causing a landslide that killed four children in South Sumatra province.