The city of Joso, north of the capital, Tokyo, was hit by a wall of water after the Kinugawa River burst its banks. Helicopter rescue teams have been plucking people from rooftops.
At least eight people are still missing and 100 need rescuing.
The rains come a day after a tropical storm brought winds of up to 125km/h (78mph) to central Aichi prefecture.
The chief forecaster at the Japan Meteorological Agency (JMA), Takuya Deshimaru, said that the rainfall was "unprecedented" for that part of Japan.
"We can say this is an abnormal situation and there is imminent serious danger," he went on.
The hardest-hit areas have been Ibaraki and Tochigi prefectures. Japan’s Meteorological Agency had put both regions on its highest level of alert.
Saori Mori, who lives close to the Tone River in the town of Abiko said the water is right up to the top of the banks now.
"We have been told to pack and prepare to evacuate as soon as we are told to," Ms Mori said, adding that she and her family were "getting ready for a fast exit".
