A typhoon killed 17 people in Japan on Wednesday, most on an offshore island, but largely spared the capital and caused no new disaster as it brushed by the wrecked Fukushima nuclear power station.

Typhoon Wipha roared up Japan's east coast, forcing the evacuation of about 20,000 people from their homes because of flooding and the cancellation of hundreds of flights.

Sixteen people were killed on Izu Oshima island about 120 kilometres south of Tokyo, as rivers burst their banks.

Meanwhile, the island's local authority says it has not been able to confirm the whereabouts of 50 of Izu Oshima's more than 8,300 residents.

The storm set off mudslides along a two-kilometre stretch of mountains.

Television footage showed roads clogged with wreckage and houses with gaping holes smashed into them.

"I heard a crackling sound and then the trees on the hillside all fell over," a woman on Izu Oshima told NHK television.

The once-in-a-decade storm brought hurricane-force winds and drenching rain to the Tokyo metropolitan area of 30 million people at the peak of the morning rush hour.

A woman was swept away by a swollen river in the west of the capital, the government said, while about 20 people were hurt in falls or struck by flying debris.

More than 500 flights at Tokyo's Haneda and Narita airports were cancelled, and thousands of schools closed. Bullet train services were halted but resumed by Wednesday afternoon.

The operator of the Fukushima nuclear plant, Tokyo Electric Power Corporation (TEPCO), cancelled all offshore work and secured machinery as the storm approached.

TEPCO has been struggling to contain radioactive leaks since a 2011 earthquake and tsunami caused extensive damage and triggered the world's worst nuclear crisis since Chernobyl in 1986.

A TEPCO spokesman said the typhoon had caused no new problems at the plant, which is on the coast 220 kilometres north of Tokyo.

The storm dumped heavy rain which had to be pumped out of protective containers at the base of about 1,000 tanks storing radioactive water, the by-product of a jerry-rigged cooling system designed to control wrecked reactors.

The rainwater was checked for radioactivity and released into the sea, the company spokesman said.

Typhoon Wipha was downgraded to a tropical depression by 5:00pm AEST. It was off the coast of north-eastern Japan and moving northeast at 95 kph, according to the Japan Meteorological Agency.

At its height, Wipha had sustained winds at its centre of 126 kph and gusts of up to 180 kph.

It was the strongest storm to hit the region since October 2004.

That cyclone triggered floods and landslides that killed almost 100 people, forced thousands from their homes and caused billions of dollars in damage.

Reuters/AFP