A typhoon has begun dumping rain on southern Japan, with strong winds, high waves and significant rainfall expected in most of the country.

Typhoon Shanshan has prompted the highest-level warnings from the Japan Meteorological Agency.

Three people have been injured and three others are missing due to a storm-related landslide and a driving accident.

The agency said the typhoon is expected to reach southern Kyushu and possibly make landfall on Thursday, and issued a high-level warning against violent winds, high waves and heavy rain for the Kagoshima prefecture.

Waves hit a coastal area in Makurazaki,
People have been urged to take shelter as the typhoon approaches the south-west (Hidetaka Komukai/Kyodo News via AP)

Shanshan was about 75 miles south of the southern island of Yakushima on Wednesday morning as it headed north toward Kyushu, packing winds of up to 112mph, according to the agency.

The warm, humid air around the typhoon and a separate high-pressure system caused heavy rain in the central Japanese city of Gamagori, where a landslide buried a house with five people inside.

Two of them were rescued alive and workers were searching for the other three, according to the Fire and Disaster Management Agency (FDMA).

People walk near a 'torii' gate of a shrine while waves hit a coastal area in Miyazak
Warnings are in place until the weekend (Hidetaka Komukai/Kyodo News via AP)

On the southern island of Amami, where the typhoon passed, one person was knocked down by a gust while riding a motorcycle, the FDMA said.

Weather and government officials are concerned about extensive damage across the nation as the typhoon slowly sweeps up the Japanese archipelago over the next few days, threatening floods and landslides and paralyzing transportation, businesses and other daily activity.

Disaster management minister Yoshifumi Matsumura, at a taskforce meeting on Wednesday, said the typhoon could cause “unprecedented” levels of violent winds, high waves, storm surges and heavy rain.

He urged residents in Shanshan’s predicted path to take precautionary measures early, such as by checking their nearest shelters, to save their own lives. Matsumura urged residents, especially older adults, not to hesitate and take shelter whenever there is any safety concern.

Someone with an umbrella in Miyazaki
Japanese officials have issued the highest weather warnings (Kyodo News via AP)

The government also cancelled its annual earthquake drills on Sunday to free up disaster response resources.

Dozens of domestic flights connecting south-western cities and islands will be cancelled through until Friday.

Japan Railway companies said most bullet trains and local train services were operating normally on Wednesday, but many on Kyushu would be suspended on Thursday.

Similar steps may be taken on the main island of Honshu until Sunday.

Postal and delivery services have been also suspended in the Kyushu region, and supermarkets and other stores announced plans to close early.