At least two people were reported dead and five others missing, police said.
Police and disaster management officials said the body of a 72-year-old woman was dug out of the debris of her home, which was smashed by a mudslide the night before in Shiga prefecture, east of Kyoto. A 77-year-old woman was found dead in a mudslide in Fukui prefecture.
Hundreds of thousands of people were ordered to evacuate across Japan.
The Meteorological Agency said the storm dumped an "unprecedented" amount of rainfall in Kyoto and two neighbouring prefectures - as much as 8 centimetres per hour.
Tourists in Kyoto were taken to safety on boats towed by rescue workers on a flooded riverside street near the scenic Arashiyama area.
The government set up an emergency task force to assess damage and support rescue efforts, said Prime Minister's Office official Hikariko Ono. Kyoto and Shiga prefecture asked the Defence Ministry to mobilise relief teams.
More than 100 people were injured across the country by Monday evening, public broadcaster NHK said, citing its own tally. A man was missing after he went to check fish traps in a river in Fukushima prefecture. A 41-year-old woman and her daughter, a fifth-grader, were missing in Mie, central Japan, apparently swept away by a swollen river.
As a preventive step, workers at the crippled Fukushima Dai-ichi nuclear power plant, about 250 kilometres northeast of Tokyo, were pumping out rainwater that was pooling around hundreds of storage tanks containing radioactive water to minimize the risk of flooding or of potential leaks from the tanks mixing with rainwater seeping into the ground or flowing to the sea.
Plant operator Tokyo Electric Power Co. said Tuesday that it moved 1,130 tons of rainwater to the ground outside of a 30-centimetre-high concrete dike around the tanks. The water was thought not to be tainted by radiation. Any rainwater containing radioactivity exceeding an allowable limit was pumped into extra tanks, TEPCO said.
The government's Nuclear Regulation Authority, however, said the pumping and release of the rainwater into the environment was possibly "an event" subject to reporting under nuclear safety rules. Regulators said they were checking TEPCO's report that the radioactivity of any released water was within allowed discharge limits.
Recent acknowledgements by officials that contaminated water is leaking from the plant have triggered safety concerns.
At Japan's Monju test reactor site in Fukui, which is currently off-line, an emergency data transmission system went down, apparently due to storm damage, regulators said Monday, an indication of risk management issues at Japanese nuclear facilities apart from the Fukushima crisis.
- AP
