A powerful typhoon slammed into Japan on Tuesday, leaving at least three dozen people injured and one missing, as torrential rains caused serious flooding that washed away a bridge and inundated homes and cars.

Transportation across southern Kyushu -- hit by deadly quakes earlier this year -- and parts of western Japan came to a standstill as Typhoon Malakas ripped across the country, packing winds of up to 180 kilometres (112 miles) per hour.

Television footage from public broadcaster NHK showed houses, cars and fields partly submerged in muddy brown water in Miyazaki prefecture, where a record 578 millimetres of rain fell on one city in just 24 hours.

Cars and pedestrians sloshed through waterlogged streets while a wall of water washed away a bridge in Kagoshima city.

NHK said at least 36 people were injured, and officials issued evacuation advisories that affected about 620,000 people.

A 66-year-old climber was missing after he reportedly fell into a swollen river that had breached its banks, local police said, adding that their search was called off due to the bad weather.

"We will resume our search tomorrow if weather permits," a police spokesman said.

More than 114,000 households lost power in Kyushu, which was rocked by a pair of deadly quakes in April that left about 50 dead.

Regional train services slammed to a halt and about 180 flights were cancelled because of strong winds from the raging storm, which was moving toward Tokyo on Tuesday afternoon with officials warning of high seas, possible landslides and more flooding.

"The winds were really powerful and they rattled windows when the typhoon landed in the city," said a spokesman for western Tanabe city.

At least half a dozen people had to be rescued from their waterlogged homes by boat.

Big storms regularly strike Japan, with 22 people killed this month when Typhoon Lionrock pounded the country.

In 2013 a powerful typhoon that triggered massive landslides on Oshima island killed 40 people, while 82 died after a typhoon hit Japan in 2011.