One person has died in Japan, while 500,000 residents were urged to evacuate and hundreds of flights were cancelled, as a powerful typhoon brought heavy rains and strong winds to its southwestern islands.

Typhoon Neoguri, which is forecast to reach Tokyo later this week, has been dowgraded from its original status as a super typhoon but the storm remained intense, with gusts of more than 250kmph.

One man was killed after his boat was swamped by high waves, NHK national television said. Several people suffered minor injuries from falls.

The typhoon was powering towards the Okinawa island chain where emergency rain and high-seas warnings were in effect, the storm will be at its most powerful as it passes over the region, about 1,600 km southwest of Tokyo on Tuesday.

The Japan Meteorological Agency (JMA) warned of heavy rains and potential flooding in Kyushu, the westernmost of Japan's main islands, as well as heavy rain in the rest of the nation as the storm turns east.

"People must take the utmost caution," Keiji Furuya, state minister in charge of disaster management, told a news conference, the Reuters news agency reported.

One man was missing after his boat was swamped by high waves, NHK national television said. Several people suffered minor injuries from falls.

More than 50,000 households in Okinawa lost power and an oil refinery halted operations. Television footage showed street lights rocking in high winds and branches being blown down largely deserted streets.

Several nuclear power plants in the affected region have been shut down due to national policy formed after the Fukushima nuclear plant was wrecked by an earthquake and tsunami in March 2011.

A JMA official said the storm will maintain its strength as it heads north but gradually turn to the east, making landfall in Kyushu before raking its way up the main island of Honshu and coming close to Tokyo on Friday.

Source: Agencies