Officials said 10 people were unaccounted for after Typhoon Nabi set off landslides, forcing the cancellation of more than 1,000 flights and disrupting Prime Minister Junichiro Koizumi's re-election campaign schedule.
Police said at least 98 people were injured, 20 of them seriously. In South Korea, five people were also reported missing.
"It was such a large amount of rain and lasted for such a long time. There was more damage than we expected," said a police spokesman in worst-hit Miyazaki prefecture, where eight died and more than 300 homes damaged.
"The major rivers in Miyazaki were about to burst. Had they done so, the damage would have been even greater," he said.
Nabi worked a slow path over the southern island of Kyushu, including Miyazaki, on Tuesday before heading onto the Sea of Japan (East Sea).
But on Wednesday it was shifting back northeast, threatening the northern island of Hokkaido which is rarely hit by typhoons.
Four days ahead of Sunday's general election, Koizumi took a break from campaigning to hold a meeting with disaster authorities to review preparations.
"We will make decisions as we look at the entire situation" of typhoon damages, the disaster management minister, Yoshitaka Murata, told reporters after meeting with Koizumi.
Rescue workers on Kyushu used long, metal rods to feel under piles of mud for any buried victims.
In the rural town of Tarumi, rescuers found the bodies of two elderly women in their 70s at a house that was engulfed by a landslide. Another dead woman had been found in the house Tuesday.
In western Yamaguchi prefecture, a landslide collapsed a section of a highway, burying three people who were inside two houses.
Residents of Hokkaido were warned of heavy rain, strong winds and high waves, with Nabi expected to hit the island by Thursday, the meteorological agency said.
The typhoon caused the cancellation of 136 domestic flights Wednesday, after a total of 894 flights were cancelled on Tuesday, according to public broadcaster NHK.
As of 1100 GMT, Nabi was above the sea 240 kilometers (150 miles) west of Oga peninsula in northern Akita prefecture, the meteorological agency said.
Packing winds of up to 90 kilometers (56 miles) per hour, Nabi was moving northeast at 50 kilometers (31 miles) per hour, it said.
Mainland Japan was struck by a record 10 typhoons last year. One of them, Tokage, was the deadliest in a quarter-century, killing 90 people.
In South Korea, an 18-year-old student was missing after heavy rains sent here car into a river, police said.
Floods also swept away a 70-year-old man and three other people went missing overnight in South Korea, Yonhap news agency reported.
About 1,000 people fled their homes in the South Korean city of Ulsan and nearby cities. The typhoon grounded 100 domestic and international flights.