A typhoon of similar strength to Hurricane Katrina hit southwestern Japan, cutting power supplies and disrupting transport and oil refineries.
Winds were gusting up to 160 km an hour at the centre of the typhoon, but the storm was expected to weaken slightly as it passes over cooler water.
Residents make their way through a flooded street in Tokyo's Suginami residential area as a powerful typhoon bearing down on southwestern Japan brought torrential rain and thunder storms to the capital during the night.
The Tropical Storm Risk website classified Nabi as a Category 4 storm on an ascending scale of 1 to 5, the same category as Katrina, which hit the US Gulf Coast last week.
Typhoon Nabi, whose name means "butterfly" in Korean, was travelling north-northwest at 15 km an hour, heading directly for the densely populated southern island of Kyushu.
The Meteorological Agency expects Nabi to swerve to the east over the next 24 hours, putting it on course to batter much of Japan and southern and eastern parts of South Korea.
Nabi has sparked thunderstorms in Tokyo, where more than 4.3 inches of rain fell in an hour in some areas late on Sunday.
Thousands of households in or near Tokyo were flooded and lost power; some highways were closed and trains delayed.
Japanese oil refiners suspended waterborne operations at some of their facilities on Monday, refinery spokesmen said.