Typhoon Halong has hit western Japan, leaving dozens of people injured while the coastguard searched for a man who went missing apparently while surfing when the storm hit.

The storm was expected to move away from the Japanese archipelago on Sunday, the Japan Meteorological Agency said, after it made landfall on the largest and most populous island of Honshu.

About 1.6 million people had been ordered to evacuate their homes ahead of the storm, local media reported.

In southwestern Wakayama prefecture, a man who was apparently surfing on the Pacific coast went missing earlier in the day, local police said.

"According to a witness, a man in a wetsuit was seen drifting about 30 metres offshore and then disappeared," said a local police spokesman.

The storm injured at least 70 people throughout the country, public broadcaster NHK said.

More than 200 flights were cancelled and some bullet trains suspended services due to the typhoon.

The weather agency had earlier issued its highest warning - meaning a threat to life and the risk of massive damage - for Mie prefecture, about 300km west of Tokyo, warning that "unprecedented" torrential rain in the areas could trigger massive landslides or major floods. The warning was lifted in the afternoon.

Houses and rice paddies were submerged in a wide area of western Japan, mainly on Shikoku island, public broadcaster NHK said.

Television footage showed trees uprooted and electricity poles toppled due to the strong wind.

Earlier this week, storms and torrential rain left one dead and 25 injured according to Japan's public broadcaster NHK.

Source: Agencies