Typhoon Neoguri slammed into Japan's southern main island early Thursday after lashing the Okinawa island chain, with three people killed as powerful winds and torrential rains battered the country.

Officials have warned of the risk of flooding and landslides, after the storm forced local authorities to advise half a million people to seek shelter in Okinawa earlier in the week.

Neoguri made landfall early Thursday near Akune City on the west of the island of Kyushu, which is home to 13 million people and lies next to the country's biggest island of Honshu where major cities including Tokyo and Osaka are located.

The typhoon's winds slowed somewhat overnight, with the storm packing gusts of up to 126 kilometres (78 miles) per hour as it moved east at 25 kilometres per hour.

But areas outside the typhoon's immediate path were still being lashed with heavy rain.

Rivers and creeks flooded in Honshu, with a mudslide swallowing a house and killing a 12-year-old boy who was inside.

"Upon receiving an emergency call on a mudslide in Nagiso Town, police and paramedics rushed there," late Wednesday, a local police official said.

"They pulled a mother and her three children out of mud and rubble... but a boy, 12, was confirmed dead at hospital," he said.

A middle-aged man in the town told public broadcaster NHK that he went out to see a river in the neighbourhood late Wednesday as he heard what sounded like "an earthquake".

"I saw rocks nearly two metres (six-foot) big rolling down... I cringed at the sight as it was the first time I've seen something like that," he said.

The government was set to hold a disaster-management meeting Thursday morning to discuss how to best cope with the storm, which is forecast to move further along the Japanese archipelago after crossing Kyushu.

Residents in remote villages and larger communities across Kyushu -- where the largest city Fukuoka has a population of more than one million -- were being urged to seek shelter before nightfall.

Shinkansen bullet-train services in Kyushu were halted and flights cancelled.

As the typhoon bore down on the archipelago, round-the-clock television footage pinpointed its latest location and helmet-clad reporters surveyed the damage left by the powerful storm.

On Tuesday, the storm claimed the life of a 62-year-old man knocked off his boat in rough waters in southwestern Kochi Prefecture, according to authorities, while NHK said an 81-year-old fisherman died in Kuammoto prefecture on Kyushu.