Powerful Typhoon Nangka lashed Japan on Friday, killing at least two people and triggering floods as authorities urged more than 230,000 residents to evacuate.

Packing gusts up to 126 kilometres per hour, Nangka barrelled over the nation's main island of Honshu after making landfall near Cape Muroto on Shikoku island late Thursday.

The storm was passing near Tottori prefecture in western Japan by Friday noon, moving north at 15 kilometres an hour towards the Sea of Japan, the Japan Meteorological Agency said.

Nangka, Malaysian for jackfruit, paralysed traffic, grounding at least 94 domestic flights, as torrential rain and violent winds swept large areas of western Japan, officials said.

Television footage showed muddy water overflowing Naka river in Tokushima flooding up to the second floor of nearby school buildings.

The weather agency has issued warnings for floods, gale-force winds, landslides and high waves in southern Japan.

Local authorities urged at least 230,000 people in the storm's path to evacuate, according to Japan's public broadcaster NHK.

A 71-year-old who was trying to reinforce window panes was found dead on Thursday in Awaji island, Hyogo prefecture, a local official said, adding a few landslides had also been reported.

"Winds are getting weaker but rain remains quite heavy," the official said. "We are still asking our residents to stay on alert."

An 85-year-old who had apparently gone out to check on farmland was found dead Thursday night in Shiso, also in Hyogo prefecture, another official said.

NHK said at least 39 people had been injured in the storm.