Typhoon Faxai landed in the coastal city of Chiba early Monday morning, causing heavy rain and wind at 120 mph, according to the Japan Meteorological Agency (JMA).
The storm then moved over Tokyo and Japan paralyzed transport. Tokyo's major subway stations were packed with commuters on Monday morning, all waiting for disused high-speed trains and subways.
Train traffic was resumed gradually in the morning, but there are still delays on all routes.
More than 100 flights to and from airports in Tokyo were canceled on Monday, including 49 flights from Japan Airlines and 41 from All Nippon Airways according to the airport website. The entire Keikyu railway connecting Tokyo and Yokohama with Haneda Airport is still out of service.
Photos show flooded streets dotted with fallen trees and branches. On Monday, workers used to burn signs and lamps that burned out, and Higashi Chiba Station employees inspected the roof, which was twisted and torn apart.
No deaths have been reported so far, but at least 10 people have been hospitalized. NHK said on Monday.
Prior to the typhoon, JMA issued warnings of storm surges, floods and landslides, and called on the public not to go outside.