Powerful typhoon killed one person, injured more than 40 and cut off land and sea transportion before heading north and weakening to a tropical storm in Tokyo.
At least three people were missing.
Authorities suspended some train services in Tokyo and warned of possible landslides and flooding in the capital and other nearby areas, advising hundreds of people to evacuate. By mid-day Friday, transportation was mostly restored in the metropolitan area.
The tropical storm, originally called Typhoon Fitow, made landfall late Thursday night in Kanagawa prefecture (state) just southwest of Tokyo, before heading north and losing power. As of Friday afternoon, it was about 300 kilometers (180 miles) northeast of Tokyo, with winds of 108 kph (66 mph), the Japan Meteorological Agency said.
The storm dumped heavy rain on parts of Japan's main island of Honshu since Wednesday - up to 600 millimeters (24 inches) in some areas.
A 76-year-old man was killed by a falling tree Thursday in Karuizawa, a resort town in central Japan, the National Police Agency said in a statement.
A 52-year-old man went missing in Kanagawa, just outside Tokyo, after leaving home to check a nearby river, the police said. Two construction workers were also missing in a mudslide in central Fukui prefecture (state). Local police said they were investigating whether the incident was related to the storm.
Police said at least 41 people have been injured, eight of them seriously.
In downtown Tokyo, more than 1,200 people near the dangerously swollen Tama River were ordered to evacuate early Friday. Firefighters also rescued homeless people camping out along another river in downtown Tokyo that was near flood stage.
Some 57,000 homes were without power in Tokyo and nine surrounding prefectures (states). Authorities issued evacuation advisories to 950 homes in south-central Shizuoka and two other prefectures, according to public broadcaster NHK.
Nearly 60 houses have been flooded in central Japan, the Fire and Disaster Management Agency said, and hundreds of public schools were closed Friday.
Fitow also grounded more than 200 domestic flights linking the capital and regional cities, affecting over 41,000 people, according to the Kyodo news agency. Airlines canceled more flights early Friday, including several international flights.
Last month, Typhoon Usagi injured more than 16 people in southwestern Japan.
Typhoon Fitow was named after a flower in Micronesia.