The death toll from floods which have devastated parts of Japan in recent days rose to seven Sunday, with thousands of homes submerged, as rescuers searched for 15 people still missing.

Police Sunday found the bodies of two men in rice paddies in Joso, the worst-hit city. Earlier in the day they discovered the body of a 68-year-old man inside a submerged car in a flooded ricefield in the town of Tochigi north of Tokyo.

Parts of Joso, a community of 65,000 residents, were washed away Thursday when a levee on the Kinugawa river gave way, flooding an area spanning 32 square kilometres (12 square miles) after the worst rains in decades.

Toru Takasugi, mayor of the city about 60 kilometres (37 miles) outside Tokyo, apologised at a press conference for not ordering residents to evacuate before the river burst its banks, local media reported.

"We thought it might break its banks but we couldn't predict where. We are deeply sorry for not handling the situation properly," he said.

Four days have passed since the flooding but a total of 1,800 rescuers including police, firefighters and military were still struggling Sunday to find 15 people still missing from Joso, public broadcaster NHK said.

The weather agency warned of the possibility of more heavy rain in the flood-hit area later in the evening.

Officials said more than 1,650 people were still at evacuation centres in Joso Sunday afternoon as over 4,000 houses were submerged and the water supply remained cut off.

The number of missing in Joso dropped from 22 to 15 Saturday after police found more victims alive, including a pair of eight-year-old children.

In Kanuma city north of Joso a 63-year-old woman was killed by a landslide, while a 48-year-old woman was found dead in the northern prefecture of Miyagi.

A 25-year-old man was killed while helping to clear blocked drains in the city of Nikko, known for its historic shrines.

Police also found the body of a man in a river in Miyagi.