Typhoon Jebi slammed into the west coast of Japan around noon on Tuesday, bringing maximum winds of 216 kilometres (135 miles) an hour and heavy rain.
Meanwhile, a 71-year-old man died after being buried underneath a storage unit that collapsed on him.
162 flights have been cancelled after the storm forced Kansai International Airport to close on Tuesday.
An aerial view shows a flooded runway at Kansai airport, which is built on a man-made island in a bay, after Typhoon Jebi hit the area.
All flights were canceled September 5, adding to the traffic chaos caused by hundreds of domestic and worldwide flight cancellations on September 4.
Television footage showed waves pounding the coastline, sheet metal tumbling across a parking lot, cars turned on their sides, dozens of used cars on fire at an exhibition area, and a big Ferris wheel spinning around in the strong wind.
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News outlets are calling the typhoon Japan's most powerful in 25 years.
Elsewhere, the winds whipped away part of the ceiling from Kyoto station and peeled off multi-storey scaffolding attached to a building in Osaka.
Many shinkansen bullet train services are back on their regular schedules for Wednesday, but there are still delays with local trains. He said electricity department officials were working overtime to restore power supply to the 240 million households that suffered a power outage.
The storm surge also created the highest tidal levels recorded since 1961, leading to flooding at the airport and forcing a shutdown.
Evacuation advisories have been issued for more than 300,000 people in western Japan - including 280,000 in the port city of Kobe - with local officials setting up some 1,500 shelters, the central and local governments said in statements.
Primary and middle schools in the storm's path were closed while regional businesses including Universal Studios Japan in Osaka and factories for several large manufacturers shut down.
The twenty-first typhoon of the season in Asia, whose winds approached 160 km/hour in its center and 220 km / h in its periphery, crossed the archipelago from the southwest to the north, where it was losing strength until becoming a storm.
Japan usually suffers the attacks of typhoons in summer, but this year has been particularly hard.