Typhoon Shanshan slammed into Japan on Thursday, injuring dozens as howling winds smashed windows and blew tiles off houses while torrential rains sparked floods and landslide warnings.

Japan's most powerful typhoon this year, packing gusts up to 252 kilometres per hour, made landfall on the main southern island of Kyushu, home to 12.5 million people, around 8am.

Ahead of the arrival, authorities issued their highest alert level in places, advising hundreds of thousands of people to evacuate and warning of "life-threatening" flooding, landslides and storm surges.

The coastal city of Miyazaki has so far recorded 26 injuries – including some from a tornado – with 124 incidents of damage to buildings, a disaster official told AFP.

Most of the injuries were caused by strong winds smashing windows, with none life-threatening.

Broadcaster NHK reported that nine people were hurt in nearby Kagoshima.

Unverified social media footage showed a small river in the city of Beppu turned into a raging torrent of dark water and a fallen tree hanging precipitously above a rainswept road near Oita.

Student Aoi Nishimoto, 18, said he had called his family in Miyazaki.

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

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

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

Kyushu's utility operator said that 254,610 houses were already without power elsewhere on the island.

The system was moving slowly, which often means more rain, with the weather office forecasting it to gradually rumble towards Japan's main island Honshu and the cities of Osaka and Nagoya, although this could change.

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."

For Kagoshima, the JMA issued "special warnings of violent storms, high waves and high tides".

"Please exercise maximum vigilance against violent storms, high waves and high tides in Kagoshima, as well as landslides, flooding in low-lying areas and overflowing rivers in southern Kyushu," it said.

For southern Kyushu, the JMA predicted an enormous 1,100 millimetres of precipitation in the 48 hours to Friday morning.

Heavy rain brought by Shanshan has been lashing large parts of Japan since Tuesday.

Three members of a family died after a landslide buried a house in Gamagori, a city in central Aichi prefecture, late Tuesday, local media reported.

The deceased included a couple in their 70s as well as a son in his 30s, while two adult daughters in their 40s survived with injuries, Kyodo News reported.

Auto giant Toyota has suspended production at all 14 of its factories in Japan. Nissan and Honda also decided to halt operations at their Kyushu plants, reports said.

Japan Airlines has cancelled 275 domestic flights for Thursday, affecting 14,893 passengers, and an additional 13 for Friday that would have carried 1,307 people.

ANA scrapped 212 domestic flights slated for Thursday, affecting 18,700 passengers, and 42 Friday flights, affecting 4,200 more.

Shanshan comes in the wake of Typhoon Ampil, which disrupted hundreds of flights and trains this month. (AFP)