The government set up an emergency task force to assess damage and support rescue effort, said Prime Minister's Office official Hikariko Ono. Kyoto and neighboring Shiga prefecture asked the Defense Ministry to mobilize relief teams.
Some 70 people were injured across the country since Sunday, NHK said, citing its own tally. Among the missing was a 77-year-old woman who disappeared since a mudslide hit her house in nearby Fukui prefecture. A man was missing after he went to check fish traps in a river in Fukushima prefecture.
More than 300 homes were flooded across the western and central Japan, according to the Fire and Disaster Management Agency. About 80,000 houses were without electricity in western and central Japan.
Trains in Tokyo and its vicinity were largely suspended and hundreds of flights were grounded.
As a preventative step, workers at the crippled Fukushima Da-ichi nuclear power plant, about 250 kilometers (155 miles) northeast of Tokyo, were pumping accumulating rain water pooling around hundreds of storage tanks containing radioactive water to the ocean. That was to avoid the risk of potential tank leaks getting mixed with rainwater seeping into the soil or flowing into the sea.
Plant operator Tokyo Electric Power Co. said the plant released what is believed to be untainted rainwater to the Pacific in order to avoid flooding near the tanks, a step that could violate safety rules, the Nuclear Regulation Authority said. TEPCO says the radioactivity in the released water was within allowed discharge limits, but duty regulators at the plant are checking.
Recent acknowledgement by officials that contaminated water is leaking from underground and storage tanks into the ocean have triggered concerns about the plant's safety.
The Meteorological Agency said the storm dumped an "unprecedented amount of rainfall" in Kyoto and two of its neighboring prefectures it passed overnight, dumping as much as 8 centimeters (3 inches) per hour. It lifted a "special warning" for the area was earlier Monday but urged residents to stay alert.
In Kyoto, where the city's major Katsura River flooded, some 260,000 people in the prefectural capital alone were told to evacuate. Hundreds of thousands of others were also ordered to evacuate across Japan.