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.
Television footage from Joso in Ibaraki showed people clinging to the rooftops before helicopter rescue teams winched them to safety.
Entire homes and cars were carried away on the torrent as the Kinugawa River burst its banks after two days of heavy rainfall. The flood waters reached as far as 8km (5 miles) from the breach.
In Tochigi, more than 500mm (19 inches) of rain fell in 24 hours in places, double the amount that normally falls there throughout the whole of September, according to Japanese public broadcaster NHK.