"As over the last two or three days, we are trying to rescue people in areas flooded with water with boats and helicopters," said Fire and Disaster Management Agency official Hideyuki Shigematsu.
Niigata prefectural police said they had found the body of a 72 year-old man who had apparently drowned near the entrance of his carpentry shop in Sanjo, about 250 kilometres (150 miles) north of Tokyo.
Later, the bodies of four elderly residents, including a 78 year-old man and an 87-year-old woman, were found separately in the prefecture, police said.
The bodies of another seven elderly people have also been recovered since the rain started falling Tuesday. They had either drowned or been crushed under landslides that destroyed their homes.
A 68-year-old woman had suffered broken bones after being trapped against her house by a landslide, police said.
As the rain continued to fall Thursday, police were searching for three missing people -- two men in Niigata and a man in Fukushima prefecture, east of Niigata, police spokesmen said.
By early Thursday, about 5,800 people had been forced to leave their homes for designated disaster shelters such as schools and community centres, the disaster agency said.
About 1,650 people had been rescued, of whom 92 were airlifted to safety, it said.
More than 1,300 Japanese troops had been called upon to assist with the rescue and clean-up, the Defense Agency said.
Another 600 disaster agency workers using 88 boats were working in the area.
Roughly 400 millimeters (16 inches) of rain has fallen since Monday in Niigata, a record for the region, the Defense Agency said.
Up to 160 more millimeters rain was expected to fall in some areas of northern Japan in the 24 hours, the agency said. A severe warning for landslides and flooding was in force.
About 136,100 households were ordered or advised to evacuate their homes, 22,900 houses experienced flood damage and at least 39 landslides were reported, officials said.
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