A powerful typhoon lashed Japan's southern main island of Kyushu on Saturday, forcing thousands of people to flee their homes and killing one, a boy who fell and drowned in a swollen river.

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Typhoon Man-yi, one of the largest storms in decades, was near the city of Miyazaki on the southern part of Kyushu at 6:45 am (0945 GMT), moving northeast at 35 kilometres an hour, Japan's weather agency said.

In Miyazaki's neighboring Kagoshima, 11-year-old Keita Kamimura drowned in a river after falling in. He was found a few hours after he fell and was later confirmed dead in hospital, police said.

"He apparently fell in the river as he tried to retrieve a ball ... while playing with a cousin," said a local police officer.

The Japanese weather agency warned of torrential rain, forecasting up to 80 millimetres per hour pounding almost all of Kagoshima prefecture.

The typhoon, which packed winds of up to 216 kilometres (135 miles) an hour and made landfall on the Osumi peninsula of southern Kyushu, was expected to move along the Pacific coast of the archipelago towards the Tokyo region.

The Japan Meteorological Agency forecast Man-yi would arrive in the Tokyo region on Sunday, warning of torrential rain, flooding and landslides.

At least 45 people were injured in the Kyushu region and the southern island of Okinawa since the typhoon approached Thursday, local authorities said.

The storm paralysed Japan's air transportation, stranding tens of thousands of passengers, including US nuclear envoy Christopher Hill, who is visiting Japan on the start of his Asian tour ahead of six-nation negotiations.

"I would expect to be getting on to the ROK (Republic of Korea) probably on Monday, rather than Sunday night because of the weather," he told reporters. "And then I go on to Beijing Tuesday morning."

The storm forced All Nippon Airways and Japan Airlines to cancel 470 flights, affecting about 50,800 passengers, Jiji Press news agency said.

In Kagoshima alone, 5,683 people were forced to evacuate their homes, while 2,110 people fled from flooding and possible landslides in neighboring Miyazaki prefecture.

In Fukuoka, northern Kyushu, 1,152 people fled 789 households.

"We are preparing for this evening as the typhoon is expected to make its closest approach to this area tonight," said a local authority in Fukuoka, where a 78-year-old woman broke her arm as she was blown over by strong winds.

The storm cut off electricity to some 740,000 households in Kyushu, according to Kyushu Electric Power Co, while Okinawa, which the typhoon has lashed since Thursday, still suffers blackouts in 10,200 households.

Television footage showed exhausted residents in Miyazaki who sheltered overnight at a community hall after evacuating their houses.

"I couldn't sleep at all here," one woman told public broadcaster NHK. "I am so worried about my home. You never know what is going to happen."

Man-yi was named after a strait that is now a reservoir in Hong Kong.

Japan and other nations in the western Pacific are hit each year by lethal typhoons. Last year, Typhoon Shanshan killed nine people in Japan and injured 300 others.