Houses are flooded in the town of Oe in Yamagata Prefecture on Thursday
Houses are flooded in the town of Oe in Yamagata Prefecture on Thursday
About 540,000 people in the Tohoku and Hokuriku regions were instructed to evacuate as of Thursday morning as torrential rain swept through the Sea of Japan coast, causing floods and landslides.

The Mogami River in Nagai, Yamagata Prefecture, spilled over its banks in the early hours of Thursday, according to the land ministry. Footage from NHK and other clips shared on social media showed flooded houses along rivers, cars partially submerged and roads filled with mud in parts of Yamagata and Niigata prefectures.

The Yamagata Prefectural Government also reported that a bridge on a prefectural road had collapsed.

In Kitakata, Fukushima Prefecture, a bridge used by East Japan Railway (JR East)'s Banetsu West Line collapsed due to heavy rain on Wednesday night.

In addition to Yamagata and Niigata, evacuation alerts were also issued for Aomori, Iwate, Fukushima and Ishikawa.

During a news conference on Thursday morning, Chief Cabinet Secretary Hirokazu Matsuno said that around 1,900 households, most of them in Niigata Prefecture and neighboring areas, have lost power, while 380 households were experiencing water supply cutoffs. Two people were missing as of Thursday morning, he added.

Heavy rainfall also prompted JR East to suspend shinkansen services throughout the day between Fukushima and Shinjo, Yamagata Prefecture.

In northern Niigata, a district in the city of Murakami where a few dozen people reside has been isolated after a landslide blocked the road leading into the area, according to the city.

"The district has been isolated and there has been a power outage and water supply has been cut off," said Saichi Matsumoto, 69, who heads the district. "We've asked the city office to provide relief supplies, including water and food."

The Meteorological Agency issued emergency warnings for various cities in Niigata, including Murakami, as well as the villages of Sekikawa and Tainai. Warnings were also issued for the town of Oguni in Yamagata Prefecture.

Meanwhile, Hakusan in Ishikawa Prefecture raised its emergency warning to the highest level on Thursday, which was also issued in place earlier in the morning for some areas in Niigata.

The land ministry and Kanazawa Prefecture's meteorological observatory announced later in the day that the Kakehashi River, which flows through Ishikawa Prefecture in the city of Komatsu's districts of Haneda, Ukawa and Yusenji, had spilled over its banks.

Such special warnings are issued when a once-in-a-decade disaster looks imminent or is feared to have already happened.

The warnings come after the agency had already issued a special emergency warning Wednesday evening after a linear precipitation zone — a band of cumulonimbus clouds that can lead to heavy downpours — formed over an area stretching from northern Niigata to Yamagata.

The warnings were issued for six Yamagata municipalities — the southern city of Yonezawa and the cities of Nanyo and Nagai, as well as the towns of Takahata, Kawanishi and Iide.

The agency downgraded the special heavy rain emergency warning for Yamagata Prefecture to a lower-class warning Thursday morning. Heavy rainfall was also predicted through Friday morning in the Hokuriku and Kinki regions and through Friday night in the Kanto-Koshin region.

Officials have continued to urge people to be on the lookout for flooding in Niigata, Ishikawa and Fukushima prefectures, and to stay vigilant and take life-saving measures when necessary as the ground remains loose in many areas hit by heavy downpours.

As of noon on Thursday, the agency has retained the second-highest Level 4 alert for some parts of Niigata Prefecture. Level 4 means that a serious disaster could occur at any time, so it is important to evacuate to safety as soon as possible.

The announcement came early, in line with the agency's new policy implemented in June aimed at improving the accuracy of forecasting of linear precipitation zones and mitigating the danger and damage caused by heavy rainfall.

In Yamagata, hourly rainfall of 100 to 120 millimeters was observed in many areas. Precipitation of 277 mm and 273 mm was observed in the 24 hours through Wednesday night in the towns of Oguni and Iide, respectively, the Meteorological Agency said.

The village of Sekikawa in Niigata saw 149 mm of rainfall in just one hour early on Thursday.