Typhoon Nabi faded into a tropical storm and headed out to sea on Wednesday after killing at least 15 people in southwestern Japan.
Eleven people were missing and 119 were injured after Nabi drenched parts of Japan's third-biggest island with more than 1,000 mm (40 inches) of rain, triggering floods and landslides, public broadcaster NHK said.
Four people were also missing in South Korea, according to Reuters.
Television pictures showed rescue workers and military personnel hunting for survivors in wrecked houses in southwestern Japan and people clearing mud out of homes, schools and other buildings.
Police said at least 52 homes were destroyed or badly damaged and about 6,000 houses were flooded. Tens of thousands of people remained in evacuation centres, NHK said.
At the height of the storm over 250,000 people fled their homes in southwestern Japan, the Yomiuri newspaper said.
Floodwaters in many areas were drawing back by Wednesday morning, officials said.
"Although there are some low-lying areas that are still flooded, a lot of the water has gone down already," said an official in Kyushu's Miyazaki prefecture, some of whose towns were particularly hard-hit.
Japan's Meteorological Agency forecast that Nabi, whose name means "butterfly" in Korean, would travel northeast over the Sea of Japan, skimming Japan's west coast and hitting the northernmost main island of Hokkaido on Thursday.
The agency warned of heavy rains, high winds and possible flooding and landslides across northern Japan.