Strong typhoon Phanfone slammed into Japan Monday, packing gusting winds and huge waves that swept three US military officials out to sea in another stark reminder of the country's vulnerability to nature.

Just over a week after a volcano killed dozens of hikers when it erupted without warning, winds of up to 180 kilometres (112 miles) per hour whipped ashore, bringing heavy rain and travel chaos throughout a swathe of the archipelago.

The storm whirled over Tokyo at around 11:00 am (0200 GMT) and then headed northeast, dumping rain further up the coast of Honshu while its eye moved out over the Pacific Ocean.

Seven people were left dead or missing, including the three US military officials who had been photographing the storm, Japanese police and coast guards said.

Typhoon Phanfone grounded more than 600 flights, and caused the cancellation of dozens of bullet train services, leaving travellers stranded in stations.

The leading edge of the storm brought a nasty commute to Tokyo's morning rush hour, with hundreds of thousands of office workers caught up in the driving rain that lashed the streets.

Localised flooding was reported while television footage showed around 15 of the 20-metre (66-foot) high poles holding up the netting at a golf driving range had collapsed, crashing into houses in Chiba, east of Tokyo.

The storm also battered Japan's auto industries.

Toyota Motor temporarily suspended operations at its 12 factories in Aichi, central Japan, due to the impact of the typhoon on its parts supplies, a company spokeswoman said, adding that production lines reopened by Monday evening.

- Risk of further flooding -

The weather agency warned that even as the storm passed out to sea landslides and floods were still a risk in a country where a relatively wet summer brought numerous landslides, including in Hiroshima where more than 70 people died.

In the central Japanese prefecture of Shizuoka, more than 50,000 people were ordered to evacuate their homes, while around 1.7 million others were advised to take refuge, local authorities said.

Three US military officials were engulfed by high waves triggered by the storm on the southern island of Okinawa.

"Three officials were taking pictures with high waves whipped up by the typhoon in the background," a local police spokesman said.

"One has been found dead, with the two others still missing," he said early Monday.

A 21-year-old surfer was also missing in the Pacific off Fujisawa, southwest of Tokyo, a coast guard spokesman said.

And rescuers were searching through the mess left by two separate landslides in Yokohama, southwest of Tokyo, where two people were missing.

A junior high school boy had also disappeared after being swamped by high waves on the coast at Yokosuka, south of Tokyo, a city official said.

About 57 people were injured across the country in storm-related accidents, public broadcaster NHK said.

Tokyo Electric Power Co., the operator of the tsunami-crippled Fukushima Daiichi nuclear power plant on the northeastern Pacific coast, said it had halted ground and sea operations, and bundled away cables and hoses.

"We are also patrolling and checking where water may flow in," a company spokesman said.

In the mountainous centre of the country, the typhoon meant the suspension of the search for the bodies of at least 12 hikers believed to be lying on the still-smouldering Mount Ontake. The mountain has already yielded 51.

The volcano was packed with walkers when it burst angrily to life on September 27, with many there to witness the spectacular colours of the countryside as summer turned to autumn.

The eruption was Japan's deadliest in almost 90 years and nearly 1,000 troops, firefighters and police have participated in a search made treacherous by the gases still rising from the peak, as well as a knee-deep layer of sticky ash.

"We want to resume operations as soon as possible when weather permits," said an official of the crisis management office of Nagano, where the volcano sits.