The deaths were in the badly hit prefectures of Tochigi and Miyagi, both north of the capital, Tokyo.
According to officials, 26 people are still missing, 25 of them in or around Joso city in Ibaraki, where the Kinugawa River burst its banks on September 10.
Officials have warned of further heavy rain and the risk of mudslides.
The torrential rain comes in the wake of Typhoon Etau, which ploughed through Japan earlier this week.
Officials have confirmed that a 63-year-old woman was killed when her house was hit by a landslide in Kanuma City in Tochigi.
A second woman, 48, was killed after her car was swept away in Kurihara city in Miyagi. And in hot spring resort of Nikko in Tochigi, a man died after falling into a drain he was trying to clear.
At least 27 people have been injured, eight seriously.
In Joso, nearly 6,000 emergency service workers are trying to reach stranded people. Many rescuers had worked through the night.
Officials in the city of 60,000, about 30 miles northeast of Tokyo, said 22 people there had lost contact after requesting help. NHK reported that two eight-year-old children were believed to be among them.
Akira Motokawa, a Joso city evacuation official, told national broadcaster NHK that rescuers had been unable to keep up with the volume of calls for help.
Thousands have been taken to temporary shelters, many carrying almost nothing with them.
Floodwaters in Joso had subsided somewhat by September 11, but much of the city was still under water and it is not clear when evacuees will be able to return home.
Takuya Deshimaru, chief forecaster at the Japan Meteorological Agency (JMA), has said the rainfall over the past few days was “unprecedented”.
In Tochigi, more than 19 inches of rain fell in 24 hours in places, double the amount that normally falls there throughout the whole of September, according to NHK.
Parts of central Tochigi have seen almost 24in of rain since September 7, breaking records.
A severe rain warning remains in effect for large areas of northeastern Japan.
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