There were also 13 people missing, public broadcaster NHK said, as Typhoon Hagibis left vast swathes of low-lying land in central and eastern Japan inundated and cut power to almost half a million homes.
Prime Minister Shinzo Abe convened an emergency meeting of relevant ministers and sent the minister in charge of disaster management to the affected areas. He offered condolences to the families of those who were killed and said the government was working to save people's lives and property.
In Fukushima, north of the capital, Tokyo Electric Power Co reported irregular readings from sensors monitoring water in its Fukushima Daiichi nuclear plant overnight. The plant was crippled by a 2011 earthquake and tsunami. Military helicopters airlifted stranded people from homes near the river, some cradling their children, after they were trapped by water reaching the roofs of their houses.
The Japan Meteorological Agency had issued the highest alert level for 12 prefectures, warning of the potential for once-in-decades rain totals, but lifted them early on Sunday.
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