At least three people were killed and 45 others were injured on Thursday in what, according to the Japanese authorities, could be one of the strongest ever storms to hit the region.

Millions of people were ordered to evacuate their homes as Typhoon Shanshan lashed southwest Japan with strong winds and torrential rain on Thursday, knocking out power, snarling air traffic and forcing major factories to close, Reuters reported.

With gusts of wind around 180 kilometres per hour, strong enough to blow over moving trucks, the typhoon was near Unzen city in Nagasaki Prefecture at 3pm and moving northwards, according to the weather agency.

It struck in Miyazaki city in southern Kyushu, shattering windows and tearing down power lines and the walls of some buildings.

Over 200,000 households in seven prefectures were without power in the afternoon, according to Kyushu Electric Power Co. The utility earlier said there was no impact at its Sendai Nuclear Power Plant in Satsumasendai city, where the storm made landfall earlier on Thursday.

Chief Cabinet Secretary Yoshimasa Hayashi told a press conference that three people had died and one was missing in incidents related to the typhoon, while the disaster management agency said 45 had suffered injuries.

After hovering over Kyushu for the next few days, the storm was expected to approach the central and eastern regions, including the capital Tokyo, around the weekend, the weather agency said.

Over 5.2 million people have been issued evacuation notices across the country, authorities said, mainly in Kyushu but also in some areas of central Japan, which have been hit by heavy rain that triggered a landslide on Wednesday.

Madoka Kubo, who runs a hotel in the historic, riverside city of Hitoyoshi in Kumamoto prefecture, told Reuters that all her reservations had been cancelled and she was now housing elderly people who had been evacuated from nearby areas.

Airlines have already announced cancellations of nearly 800 flights and train services have been suspended in many areas of Kyushu, while hundreds of bus and ferry services have also been halted, according to the transport ministry.

Typhoon Shanshan is the latest harsh weather system to hit Japan, following Typhoon Ampil, which also led to blackouts and evacuations, earlier this month.