A strong typhoon made landfall Thursday night on Shikoku, leaving two people dead and a number of other people injured.
Authorities urged hundreds of thousands of people there and elsewhere to evacuate, while transportation services were crippled.
Typhoon Nangka landed near Cape Muroto in Kochi Prefecture around 11 p.m., causing heavy rain to fall across a wide area from Shikoku to the Tohoku region.
The Meteorological Agency said the typhoon is expected to move northward into the Sea of Japan, and warned of heavy rain and strong winds that may last for hours as it was moving slowly.
Fears of landslides and flooding prompted local governments in Kochi and elsewhere to advise at least 367,800 people to evacuate their homes.
In Hyogo Prefecture, a 71-year-old man died after sustaining head injuries while trying to reinforce window glass, and the body of an 85-year-old man who had apparently gone out to check on a canal for farmland has been found.
In the village of Kawauchi, Fukushima Prefecture, the hourly rainfall reached 77.5 mm, a record there for the month of July, while winds of at least 144 kph were recorded at Cape Muroto.
The storm caused flights and railway services to be canceled or suspended mostly in western Japan.
Shikoku Railway Co. shut down all services Thursday evening, and West Japan Railway Co. plans to suspend many of its services on Friday.
The Japan Railway group operated its shinkansen trains on Thursday.
Airline service has also been severely affected. All Nippon Airways and Japan Airlines together canceled a total of 177 flights on Thursday, including those connecting Tokyo and Shikoku. Budget carriers Peach Aviation and Jetstar canceled 42 flights, including international services.
ANA, JAL and other airlines have also already canceled dozens of flights Friday as well.
Parts of expressways have been closed and ferry services also canceled due to high waves and heavy rain.
The weather agency forecasts rainfall totaling 400 mm on Shikoku and in the Tokai region around Nagoya and 500 mm in the Kinki region centering on Osaka in the 24 hours through midnight Friday. Precipitation of 250 mm is forecast in Tokyo and its surrounding region.
At 3 a.m. Friday, the typhoon was located near Kanonji, Kagawa Prefecture, and was heading north-northwest at a speed of 20 kph. The storm had an atmospheric pressure of 975 hectopascals at its center.