At least 14 people were killed, with a more than a dozen others missing, officials said.
The storm on Wednesday was headed toward Japan's northern island of Hokkaido, where up to 25cm of rain was expected by early Thursday, the Meteorological Agency said.
Typhoon Nabi slammed into southern Japan on Tuesday, flooding towns and driving more than 300,000 people from their homes.
About 1500 soldiers were deployed to fortify coastal defences and help in the rescue effort.
Nabi lost strength on Wednesday as it roiled over the Sea of Japan and was downgraded to a tropical storm.
But it still was churning winds of up to 108km per hour, the agency said.
Authorities in Japan said at least 14 people were killed in mudslides and flooding, while 15 others were unaccounted for.
A record 10 typhoons and tropical
storms struck Japan last year
National broadcaster NHK reported its own toll of 15 dead and 11 missing in Japan.
South Korea's National Emergency Management Agency said two people were missing there, while the country's Yonhap News Agency said the whereabouts of five people were unknown.
More than 70,000 homes, mainly on Kyushu island, were still without electricity on Wednesday afternoon, power companies said.
Japan Airlines and its affiliates cancelled 47 flights on Wednesday morning, while All Nippon Airlines grounded 43 flights, affecting almost 12,000 people.
Flights returned to normal in the afternoon, the two companies said.
Nabi, meaning butterfly in Korean, also caused damage in South Korea, dumping up to 35cm of rain in southern and eastern parts of the country from Monday to Wednesday morning.
Last year, a record 10 typhoons and tropical storms struck Japan, leaving nearly 220 people dead or missing, the largest casualty toll since 1983.