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.
The powerful gusts ripped sheeting from rooftops, overturned trucks on bridges and swept a 2,591-ton tanker anchored in Osaka Bay into a bridge leading to Kansai International Airport.
The damage to the bridge left the airport, which is on an artificial island, cut off from the mainland, and around 3,000 people were stranded at the facility overnight, a transport ministry official told AFP.
Parts of the airport’s runways and basement were also flooded after high waves whipped up by the storm washed into the facility.
On Wednesday morning, a boat service was ferrying people from the airport to nearby Kobe, the transport ministry official said.
But there was no indication yet when the airport, which runs over 400 flights a day, might reopen.
"We had a blackout so there was no air conditioning. It was hot," a woman transported Wednesday by boat to Kobe Airport told public broadcaster NHK.
"I’d never expected this extent of damage from a typhoon."
NHK said the toll in the storm stood at nine, with Jiji news agency saying five of the dead were in Osaka prefecture.
Hundreds more were injured, mostly by flying debris, local media said.
Evacuation advisories were issued for more than 1.22 million people as of Wednesday morning, while another 29,600 people under stronger, though still not mandatory, evacuation orders, the Fire and Disaster Management Agency said.
And 16,000 people spent the night in shelters across 20 prefectures, Jiji reported.
The fast moving typhoon left land on Tuesday night, moving offshore from the central Ishikawa region, but it left a trail of destruction in its wake.
In Kyoto, it brought down part of the ceiling of the tourist magnet’s main station, and in Osaka, the high winds peeled scaffolding from a multi-story building.
Footage on NHK showed a 100-metre (328-foot) tall ferris wheel in Osaka spinning furiously in the strong wind despite being switched off.
"I’ve never seen such a thing," a 19-year-old man at the scene told NHK.
Up to some 2.3 million households suffered blackouts and businesses, factories and schools in the affected area shut down while the storm crossed the country.
Nearly 800 flights were cancelled, including several international flights departing and arriving at Nagoya and Osaka, along with ferries, local train services and some bullet train lines.
Prime Minister Shinzo Abe had urged people to evacuate early and ordered his government to take all necessary measures to protect residents.
"I urge the Japanese people to take action to protect your lives, including preparing and evacuating early," he said.
Japan is regularly struck by major storms during the summer and autumn.
The country has been sweating through a record deadly heatwave that followed devastating rain in parts of central and western Japan that killed over 200 people.
The sustained rain caused widespread flooding and landslides in July, devastating entire villages and forcing thousands from their homes.
The flooding and landslides proved so deadly in part because many people did not heed evacuation warnings, which are not mandatory.
Since the disaster, authorities have urged people to take the warnings more seriously and prepare to leave home immediately they are issued.