Police said they found the body of a 68-year-old man in Tochigi, north of Tokyo, in the early morning, the fifth located in the rescue operation.
The body was reportedly found inside a submerged car at a water-covered rice field in the town that also suffered floods.
Police also discovered another body of a man in the afternoon in a rice field of most severely-hit Joso, a community of 65,000 residents, parts of which were washed away Thursday when a levee on the Kinugawa river gave way, flooding an area that reportedly spans 32 square kilometres (12 square miles) after the worst rains in decades.
Four days have passed since the flooding but search operations continued Sunday with a total of 1,800 rescuers including police, firemen, and the Self-Defence Forces scrabbling to find 15 people still missing from the town, public broadcaster NHK said.
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The clock is ticking as the area expects heavy rain in the evening, which could further spread the water damage.
Officials said more than 2,100 people were still at evacuation facilities in Joso Sunday morning as over 4,000 houses were submerged and water supply was cut off.
In Kanuma city, north of Joso, a 63-year-old woman was killed in a landslide, while a 48-year-old woman was also found dead in Miyagi prefecture, northern Japan.
The third victim was a 25-year-old man helping to clear clogged drains in the city of Nikko, which is known for its historic shrines.
Police also found the body of a man in another river in Miyagi who was believed to be a 62-year-old missing from the prefecture, according to local media.