Heavy rain pounded a wide swath of Japan on Friday, prompting flood warnings and evacuation orders that affected millions of people and leaving a man dead, with the weather agency warning of continuing downpours into the weekend.

The rain also disrupted transportation services, including cancellations of shinkansen bullet train services in some areas as well as flights into and out of Japan's southern prefecture of Okinawa.

The severe weather conditions have been caused by warm and moist air blowing from near Typhoon Mawar, which is passing south of the country, and a rain front hanging over Japan's main island Honshu.

Thunderstorms were observed developing one after another in six prefectures, causing concentrated heavy rainfall, including in the western prefectures of Kochi, Nara and Wakayama.

A car is partially submerged in a flooded street in the western Japan city of Wakayama on June 2, 2023. An approaching typhoon brought torrential downpours that prompted evacuations in parts of Japan the same day. (Kyodo) 

Rising water levels of rivers prompted some local governments, such as Toyohashi in Aichi Prefecture and Iwata in Shizuoka Prefecture, both in central Japan, to issue the highest level of warning to residents, calling on them to immediately ensure their safety.

In Toyohashi, a man apparently in his 60s was pronounced dead early Saturday after being found inside a car in a flooded agricultural field Friday night, police said, adding that water had nearly filled the inside of the vehicle.

In Wakayama Prefecture, police and firefighters searched for individuals believed to have been swept away near a river and on a flooded road. A woman in her 80s also sustained injuries after falling over when trying to evacuate.

JR Central temporarily suspended all services of its Tokaido Shinkansen line, which connects Tokyo and Osaka, before resuming operation of the section between Shin-Osaka and Nagoya stations.

Service between Tokyo and Nagoya in Aichi Prefecture on the line remained suspended throughout Friday, with the operator saying on Saturday it will resume in the afternoon.

A resident walks down a flooded street in the western Japan city of Wakayama on June 2, 2023. An approaching typhoon brought torrential downpours that prompted evacuations in parts of Japan the same day. (Kyodo) 

Among those affected by the bullet train cancellations at Tokyo Station was Chie Fujii, 45, from Okayama, western Japan. She had spent the night in the capital to take part in a handicraft class. "I really need to get home for work tomorrow, so it's a real shame," she said.

In Gifu, Shizuoka, Aichi and Mie prefectures, at least 2 million people were temporarily advised to evacuate.

The Japan Meteorological Agency reported record rainfall in some areas in the six hours through 9 p.m., with 291 millimeters falling in part of Tosashimizu in western Japan's Kochi Prefecture and 240 mm in Tahara in Aichi Prefecture.

The agency says it expects the heavy rain to continue falling into Saturday over an area spanning western to northern Japan, and it is urging vigilance, including against landslides and overflowing rivers.

In the 24-hour period ending at 6 p.m. Saturday, the agency is forecasting as much as 250 mm of rain in the central Tokai region, 200 mm in Tokyo and nearby prefectures, 150 mm in the western Shikoku region and the Izu island chain south of Tokyo, and 100 mm in the western Kinki region centering on Osaka Prefecture.

A person walks in heavy rain in the western Japan city of Kochi on June 2, 2023. The Japan Meteorological Agency projected heavy rain over a wide area of Japan through the following day due to an approaching typhoon. (Kyodo) 

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