Typhoon Halong has moved back out to sea after making landfall in the Kouchi prefecture, leaving one person dead and as many as 30 injured in its wake.
Originally a typhoon, Halong was downgraded to a tropical storm as it approached the southwest coast and made two landfalls - over Shikoku Island and Hyogo prefecture in western Japan.
It existed over the Sea of Japan from the northern coast near Kyoto on Sunday evening, and was expected to lose further strength over the next 12 hours.
The storm was off the northern coast of Wajima City, about 400 kilometers (250 miles) northwest of Tokyo, on Sunday night.
The tropical storm dumped a meter of rain in an hour. The authorities warned the public that it could trigger landslides or major floods.
“We're concerned about the softened ground due to the record-breaking rain in the region, and we don't even know yet the full extent of the damage as the typhoon is still passing through Japan," Japanese Disaster Prevention Minister Keiji Furuya said.
"I strongly urge strict caution on the possible landslides that can cause direct human damage," Furuya added.
As the storm approached, more than 1.5 million people were told to evacuate their homes as winds of up to 180kmh slowly moved northeast.
Japan's Meteorological Agency lifted a heavy rain alert for Mie prefecture in central Japan, and evacuation orders for most residents in the region and other areas were withdrawn.
More than 200 flights were cancelled and some bullet trains suspended service.
About 200,000 people were still subject to evacuation in some areas later Sunday.
At least one person was killed, washed away in a raging river, while a surfer was missing off the coast. More than 30 were injured.
The storm also flooded about 330 homes and damaged 70 others in western Japan, according to The Associated Press.
Tropical Storm Halong also disrupted land and air traffic as Japan began its annual "Obon" Buddhist holiday week. Roads were flooded and more than 200 flights canceled.
Travelers were stranded at airports and stations as they set off for Japan's annual summer holiday.
And there's more misery to come as about 40 centimeters of rain and heavy winds are forecast for eastern Japan.
Some information for this report provided by Reuters and AP.