The windows of a convenience store in Fukuoka, Japan are taped up in anticipation of Typhoon Shanshan's arrival (Yuichi YAMAZAKI)

One of Japan's strongest typhoons in decades dumped torrential rain across southern regions on Thursday, with one person missing and authorities warning of life-threatening flooding and landslides.

Typhoon Shanshan packed gusts of up to 252 kilometres (157 miles) per hour as it smashed into Japan's main southern island of Kyushu early Thursday, making it the most powerful storm this year and one of the strongest at landfall since 1960.

The storm then weakened, with maximum gusts of 162 kph at 3:00 pm (0600 GMT), the weather office said, but it was still dumping heavy rain across Kyushu and beyond as it moved slowly towards the main island of Honshu.

The Japan Meteorological Agency (JMA) warned that "the risk of a disaster due to heavy rain can rapidly escalate in western Japan as Friday approaches".

Even before Shanshan hit, precipitation pummelled large parts with three members of the same family killed in a landslide late Tuesday in Aichi prefecture around 1,000 kilometres (600 miles) from Kyushu.

Authorities issued their highest alert in places, with more than five million people advised to evacuate, although it was unclear how many did.

Kunisaki city in the Oita region of Kyushu warned inhabitants to "evacuate to a safe place or higher place such as the second floor of your houses" because of the risk of flooding.

One person was missing on Thursday -- reportedly a man on a small boat -- and two people were seriously injured, chief government spokesman Yoshimasa Hayashi said.

Rains turned rivers into raging torrents while winds smashed windows and blew tiles off roofs. TV images showed flooded roads and power lines being repaired.

The coastal city of Miyazaki, littered with debris from nearly 200 damaged buildings, reported 25 injuries -- including some from a tornado.

Some parts of Miyazaki prefecture saw record rains for August, with the town of Misato recording a staggering 791.5 millimetres (31 inches) in 48 hours, the JMA said.

Worried student Aoi Nishimoto, 18, said he had called his family in Miyazaki to see if they were safe.

"Our home is fine, but there was a tornado in Miyazaki and power went out in some places," he told AFP in Kyushu's main city of Fukuoka.

"This year, I am away from my parents' home for the first time. So it's a bit scary being all alone," fellow student Rio Ohtsuru, 19, told AFP.

"Maybe I will look for a flashlight in case of a power outage," she said.

Kyushu's utility operator said 235,760 houses were without power elsewhere on the island.

- Climate change -

Shanshan comes in the wake of Typhoon Ampil, which dumped heavy rain that disrupted hundreds of flights and trains this month but caused only minor injuries and damage.

Typhoons in the region have been forming closer to coastlines, intensifying more rapidly and lasting longer over land due to climate change, according to a study released last month.

Another released by World Weather Attribution (WWA) on Thursday said that climate change turbocharged Typhoon Gaemi, which killed dozens of people across the Philippines, Taiwan and China this year.

In the city of Usa, retiree Fukashi Oishi looked forlornly at an old tree opposite his house that was already mature when he was a child but had snapped and fallen on the road.

"Oh, it's so sad," he told AFP.

- Toyota halt -

Auto giant Toyota suspended production at all 14 of its factories in Japan.

Nissan and Honda also halted operations at their Kyushu plants, as did chipmakers including Tokyo Electron, reports said.

Kyushu is a hub for the semiconductor industry, with chip giant Taiwan Semiconductor Manufacturing Company opening a plant there in February.

Japan Airlines and ANA cancelled more than 500 domestic flights for Thursday and Friday, affecting almost 40,000 passengers.

Rail operators suspended Shinkansen bullet trains on and Kyushu and said services would be disrupted elsewhere on Friday.