Typhoon Jebi crashed into the west coast of Japan around noon on Tuesday, with maximum winds of 216 kilometers (135 miles) per hour and heavy rains.
The powerful bursts tore plates from rooftops, overturned trucks on bridges and swept a 2,591-tonne tanker anchored in Osaka Bay on a bridge that leads to Kansai International Airport.
The damage to the bridge left the airport, which is located on an artificial island, isolated from the mainland, and around 3,000 people were stranded in the facility during the night, an official of the Ministry of Transport told AFP.
Parts of the airport's runways and basement were also flooded after the storm dragged high waves to the facility.
On Wednesday morning, a boat service transported people from the airport to nearby Kobe, said the official of the Ministry of Transport.
But there were still no indications that the airport, which manages more than 400 daily flights, could reopen.
"We had a blackout so there was no air conditioning, it was hot," said a woman transported by boat to Kobe airport on public broadcaster NHK on Wednesday.
"I had never expected this extension of the damage of a typhoon."
NHK said the death toll in the storm was nine, and Jiji news agency said five of the dead were in Osaka prefecture.
Hundreds more were injured, mainly by flying debris, local media said.
On Wednesday morning, evacuation notices were issued for more than 1.22 million people, while another 29,600 people received stricter, but not mandatory, evacuation orders, the Fire and Disaster Management Agency said.
And 16,000 people spent the night in shelters in 20 prefectures, Jiji said.
The winds bring down the roof
The fast-moving typhoon left the land on Tuesday night, moving towards the sea from the central Ishikawa region, but left a trail of destruction in its wake.
In Kyoto, it demolished part of the roof of the tourist magnet's main station, and in Osaka, strong winds peeled scaffolding from a multi-storey building.
Images in NHK showed a 100-meter (328 ft) tall Ferris wheel in Osaka turning furiously in the strong wind despite being off.
"I've never seen anything like it," said a 19-year-old man on the scene to NHK.
Up to 2.3 million homes suffered blackouts and businesses, factories and schools in the affected area closed as the storm crossed the country.
Nearly 800 flights were canceled, including several international flights departing and arriving in Nagoya and Osaka, along with ferries, local train services and some bullet train lines.
Prime Minister Shinzo Abe urged people to evacuate early and ordered his government to take all necessary measures to protect the residents.
"I urge the Japanese to take measures to protect their lives, including preparation and early evacuation," he said.
Japan tends to suffer heavy storms during summer and autumn.
The country has been sweating through a record heat wave that followed a devastating rain in parts of central and western Japan that killed more than 200 people.
The sustained rain caused widespread flooding and landslides in July, devastating entire villages and forcing thousands of people to leave their homes.
Flooding and landslides proved to be so deadly in part because many people did not heed the evacuation warnings, which are not mandatory.
Since the disaster, authorities have urged people to take warnings more seriously and prepare to leave home immediately after they are issued.