Nearly 90 others suffered injuries, most of them minor, media reported.
A rapidly weakening typhoon Lan made landfall in Japan on Monday, setting off landslides and flooding but leaving the capital, Tokyo, largely unscathed, although at least two people were reported killed and train and plane services disrupted.
It had weakened to a category 2 storm when it made landfall early on Monday, sideswiping Tokyo, after it had powered north for days as an intense category 4 storm, according to the Tropical Storm Risk monitoring site. Lan is the Marshall islands word for “storm”.
At least two people were killed, one a man in his 60s who was passing a building site when scaffolding collapsed on top of him and the other a fisherman tending to his boat, Kyodo news agency said. Nearly 90 others suffered injuries, most of them minor, media reported.
Another man was missing after a landslide engulfed his home, NHK public television said, although his wife was dug out by rescuers.
Rivers burst their banks in several parts of Japan and fishing boats were tossed up on land. A container ship was stranded after being swept onto a harbour wall but all 19 crew members escaped injury.
The centre of the storm was northeast of Tokyo on Monday morning and it was moving northeast at 65 km/h (40 mph), the Japan Meteorological Agency said. It was expected to move out into the Pacific later on Monday and become a tropical depression on Tuesday.
Around 350 flights were cancelled and train services disrupted over a wide area, although most commuter trains were running smoothly in Tokyo.
Tens of thousands of people were advised to evacuate, and several thousand ordered to move, on Sunday as the storm approached, lashing a wide swath of Japan with torrential rain and wind. Those numbers had fallen sharply by Monday morning.
Toyota Motor Corp cancelled the first shift at all of its assembly plants and said that it would decide on a later shift around noon on Monday.