The Japanese government has advised almost three million people to evacuate after heavy flooding this week killed three people and left 16 people missing in the eastern region, the media reported on Saturday.
At least 27 people have been injured across 10 prefectures since floods inundated parts of eastern Japan after a tropical storm Etau, the fire and disaster management agency said.
Rescue operations continued in Joso city, one of the worst-hit areas, although floodwaters are receding, the agency added.
Rescue teams in Osaki city battled to save residents on Friday after a section of a levee containing the Shibui river broke, CNN reported.
In some areas during the past two days, residents were forced to their rooftops, desperately awaiting rescue by military helicopters.
"Tochigi prefecture is facing a grave danger and is in an emergency situation," Japan Meteorological Agency Spokesman Takuya Deshimaru said.
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"It is experiencing unprecedented downpour."
Fukushima prefecture, which was devastated by the 2011 tsunami, saw more than 30 cm of rain in 48 hours -- the heaviest downpour there in 50 years.