Two men were killed and another remains missing, officials said Tuesday, after Typhoon Vongfong smashed through Japan leaving the country counting the cost of the latest natural disaster.

The typhoon churned through eastern Japan early Tuesday after hitting Okinawa over the weekend and making landfall on the nation's southern main island of Kyushu on Monday, the meteorological agency said.

At least 96 people were injured in typhoon-related accidents in 23 prefectures, nearly half of Japan's provinces, public broadcaster NHK said.

The body of a 90-year-old man was found in a farm ditch in Tottori, western Japan, a spokesman with the Tottori Police Department said.

"We suspect the man fell accidentally into the ditch late Monday due to the storm," the spokesman told AFP.

A 72-year-old man was also found dead early Tuesday in Ehime, western Japan, after his small truck fell into a pond Monday, the local police said.

A Chinese man has been missing in Shizuoka, central Japan, since he was swept away by high waves over the weekend, officials said.

The storm was downgraded to an extra-tropical depression by mid-morning and was moving away from Japan. It was located off the coast of northeastern Japan at 0300 GMT.

Heavy rain hit the tsunami-crippled Fukushima Daiichi nuclear power plant on the northeastern Pacific coast, "but we have not received any reports of damage or abnormality", said a spokesman with Tokyo Electric Power.

Television footage the roof of a house crushing a car in Hiroshima, western Japan, and flooded roads in Sendai, northeastern Japan.

Airlines plan to cancel 78 flights Tuesday after the typhoon grounded 644 services the previous day, NHK said.

The typhoon came just a week after another storm whipped through the country, leaving 11 people dead or missing.

The latest storm forced the suspension of the search for the bodies of at least seven hikers believed to remain on the still-smouldering Mount Ontake, which erupted at the end of September, killing more than 60 people.