The year’s 18th typhoon shot through central and northeast Honshu on Monday, unleashing torrential rain and strong winds on much of the main island, including Fukushima Prefecture, where radioactive water was discharged to prevent the troubled complex from flooding.

According to local police tallies, Typhoon Man-yi had left at least three people dead and four missing before churning its way toward Hokkaido.

After making landfall shortly before 8 a.m. near Toyohashi, Aichi Prefecture, the typhoon raised havoc in five prefectures spanning the Chubu and Kinki regions, triggering evacuation orders for around 498,000 residents due to the risk of mudslides and flooding.

Warning of “unprecedented heavy rain,” the Meteorological Agency issued “special warnings” to Fukui, Kyoto and Shiga, using a new warning system launched last month for the first time.

In Kyoto alone, some 268,000 residents were ordered to leave, including about 81,000 in Fukuchiyama.

While the agency had lifted all of its special warnings by noon, the evacuation order in the city of Kyoto wasn’t lifted until late afternoon due to the scale of the floods.

Local police said they found the body of a 71-year-old woman after her house collapsed in a mudslide early Monday in Ritto, Shiga Prefecture. Another woman, 77, died after a mudslide wrecked her home in the town of Mihama, Fukui Prefecture.

Two men remained missing after being swept away in rivers in Aichi and Fukushima, while the whereabouts of a 41-year-old woman and her 10-year-old daughter was unknown after their car was found abandoned on a road along a river in Tsu, Mie Prefecture.

According to the Fire and Disaster Management Agency, 70 people sustained light or serious injuries from the bad weather and nearly 1,500 houses were flooded.

In the area around the Katsura River, which overran its banks, the flooding was so bad that Kyoto Gov. Keiji Yamada asked the Self-Defense Forces for help. At one point, the famed Togetsukyo (moon crossing) Bridge in the Arashiyama district was nearly submerged as the water damaged shops and homes in the area.

In addition, Kyoto residents reported damage along the banks near the Sanjo Ohashi bridge, the terminus of the famed Tokaido road between Kyoto and Tokyo that crosses the Kamo River downtown.

“A popular meeting area for performances and civic demonstrations just south of the bridge on the western banks was damaged,” said British resident Michael Lambe, author of the Deep Kyoto blog, a guide to the city.

Other businesses, including cafes and restaurants by the Kamo River, reported flooding as well. Kyoto’s bus and subway services, already strained with passengers from the three-day weekend, were disrupted.

According to the Meteorological Agency, precipitation in the 48 hours through Monday morning reached about 300 mm in parts of the cities of Kyoto and Otsu — more than they usually get for the entire month.

Precipitation topped 500 mm in parts of Mie and Nara, the agency said.

In Osaka, about 290,000 residents in the city’s harbor area were forced to flee early Monday. Although the evacuation order was lifted that afternoon, officials warned that the raging river currents were still dangerous.

“Water levels along the bands of the Yodo and Yamato rivers are still high, so people should not venture too close,” Osaka Mayor Toru Hashimoto said Monday afternoon.

Gusts in Saitama and Gunma, meanwhile, broke windows and caused other damage to property as the typhoon sped northeast.

As of 9 p.m., Typhoon Man-yi had weakened to an extratropical cyclone off Hokkaido, where up to 150 mm of rain was projected to have fallen by late Tuesday afternoon, the agency said.

Transportation was snarled nationwide. Train services were suspended in parts of the Tokaido, Joetsu and Nagano bullet train lines, while expressways were closed in some areas and airline flights scrubbed.

The central government formed an information liaison office within the crisis management center at the prime minister’s official residence on Monday morning.