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Three people were reported killed, hundreds of plane flights cancelled, and train services disrupted in the wake of Lan, which had maintained intense strength until virtually the time it made landfall west of Tokyo in the early hours of Monday.
The deaths included man in his 60s who was passing a building site when scaffolding collapsed on top of him and another a fisherman tending to his boat. The third was killed when a landslide engulfed his home, media reported.
Two others were left comatose by injuries and one man was missing, NHK public television said. Nearly 90 others suffered minor injuries.
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.
Some 80,000 people in Koriyama, a city 200km north of Tokyo, were ordered to evacuate as a river neared the top of its banks, NHK said, and several hundred houses in western Japan were flooded.
"My grandchild lives over there. The house is fine, but the area is flooded, and they can't get out," one man told NHK.
Lan had weakened to a category 2 storm when it made landfall early on Monday, sideswiping Tokyo, after powering 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".
The centre of the storm was out in the Pacific northeast of Tokyo on Monday afternoon and it was moving northeast at 75km/h, the Japan Meteorological Agency said.
It was expected to become a tropical depression on Tuesday.
About 350 flights were cancelled and train services disrupted over a wide area of Japan, although most commuter trains were running smoothly in Tokyo.
Toyota Motor Corp cancelled the first shift at all of its assembly plants but said it would operate the second shift as normal.