A tropical storm has injured 16 people and knocked out power to tens of thousands of homes across southwestern Japan, forcing the evacuation of nearly 400,000 residents and grounding hundreds of flights as it moves toward the mainland.

Storm Jangmi, which was earlier a typhoon, battered the subtropical island of Okinawa on Monday before moving north toward Kyushu, Japan's southernmost main island.

The Japan Meteorological Agency warned of high waves, landslides and flooding as the storm continued northward.

Around 17,000 households in Okinawa and more than 30,000 in the southwestern Kagoshima region were without power on Tuesday morning.

The storm was located about 140km west-southwest of Yakushima island in Kagoshima prefecture at around midday on Tuesday, moving northeast at 30kmph with a central pressure of 975 hectopascals, packing sustained windspeeds of up to 90kmph and gusts up to 126kmph.

The entire population of Miyazaki city on Kyushu, around 390,000 people, were urged to evacuate. Injuries in Okinawa were caused by flying objects striking cars and strong winds knocking people off their feet, public broadcaster NHK reported. A 10-metre tree was felled by the storm's winds.

Japan's top government spokesman Minoru Kihara warned that public transport in Tokyo and nearby cities could face disruptions on Wednesday as the storm approaches.

"For those of you living in areas likely to be affected by the storm, please pay close attention to evacuation information issued by your municipalities, and stay mindful of early evacuation," Mr Kihara said at a news conference. "Please remain vigilant and make sure you take action to protect your life."

Japan's two largest airlines, All Nippon Airways and Japan Airlines, cancelled a combined 600 flights scheduled between Monday and Wednesday. Further disruptions are expected for routes serving Kyushu and the island of Shikoku.

Forecasters say rainfall totals in affected regions could reach 200 to 300mm, with western Japan regions such as Shikoku and Kansai expected to receive up to 300mm by noon on Wednesday, while central Japan including Tokai and Kanto could see 200mm.

Earlier, authorities warned people in the affected areas to brace for violent storm winds, high waves, landslides, flooding and overflowing rivers.

The storm was expected to move northeast along the Pacific coast through Wednesday, after which the typhoon may weaken, the meteorological agency said.

The government has set up an information liaison office at the cabinet’s disaster management centre and will coordinate with local governments to share information on evacuation services and weather forecasts, Mr Kihara said.