Tropical Storm Halong disrupted land and air traffic as Japan began its annual "Obon" Buddhist holiday week.
The storm-hit Japan was also shaken this afternoon by a magnitude-6.1 earthquake that struck off the northeastern coast near Aomori.
There was no danger of a tsunami, and no damage or injuries have been reported. The Nuclear Regulation Authority said nuclear facilities in the area remained intact.
Originally a typhoon, Halong was downgraded to a tropical storm as it approached southwest coast and made two landfalls over Shikoku Island and Hyogo prefecture in western Japan. It was on track to exit into the Sea of Japan from the northern coast near Kyoto later today, and further lose strength in the next 12 hours.
Japan's Meteorological Agency issued the highest alert for heavy rain in Mie prefecture in central Japan, prompting two towns to order about 570,000 residents to move away from swollen rivers.
Another 600,000 people were advised to evacuate across the country. Some of the evacuation advisories in western Japan were later lifted as the storm moved farther north.
In Iwate, northern Japan, a 78-year-old man was found dead late Saturday after plunging into a swollen irrigation canal at his farm. In Miyazaki, southern Japan, a woman in her 70s broke her ankle as a portable toilet booth fell on her while she was walking by.
Japan's public television NHK said 52 people were injured. More than 200 flights were canceled, stranding thousands of holidaymakers at airports around the country. The rainstorm also flooded some 330 homes and damaged 70 others in western Japan.
The storm, packing winds of up to 100 kilometers (60 miles) per hour, was expected to dump 30 centimeters (12 inches) of rain in central Japan by tomorrow. The meteorological agency warned of landslides and floods, and predicted heavy rain and strong wind in Tokyo and northern Japan through Monday.
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