A powerful storm slammed into Japan on Sunday, churning across western areas already hard hit by floods and landslides earlier this month and injuring some 20 people.
Typhoon Jongdari, with winds of up to 180 kilometres (110 miles) an hour, made landfall at Ise in Mie prefecture at around 1 am (1600 GMT Saturday), according to the meteorological agency.
More than 170 domestic flights were cancelled for Sunday and train services disrupted.
A total of 21 people have been injured in the past days as the storm brought violent winds and torrential rains, the government said.
Prime Minister Shinzo Abe warned that the storm could continue to bring heavy rain even after the epicentre had passed by.
"Get hold of information on damage, cooperate closely with municipal offices and make utmost efforts to help evacuate local residents," he central government officials on Sunday.
The typhoon weakened after making landfall and was downgraded to a tropical storm but many provinces stayed on alert.
"We have been on emergency alert the whole time since the rain disaster" in early July, said Koji Kunitomi, a crisis management official in the western prefecture of Okayama.
"Fortunately, so far, we haven't seen new flooding," he told AFP.
The storm, after unleashing torrential rain over eastern and Japan, moved west and then south on Sunday.
TV footage showed high waves smashing onto rocks and seawalls southwest of Tokyo and trees buffeted by strong winds and heavy rain.
Waves shattered the window of an ocean-view restaurant at a hotel in the resort town of Atami southwest of Tokyo late Saturday.
"We didn't expect this could happen... Waves gushed into the restaurant as the window broke but we are grateful that customers followed evacuation instructions," an official at the hotel told AFP.
"Fortunately no one was seriously hurt," she said, adding five people suffered cuts from broken glass as they fled.
The storm moved across the western region of Chugoku, where record rainfall early this month unleashed flooding and landslides which killed around 220 people.
It was Japan's worst weather-related disaster in decades, and thousands of those affected are still in temporary shelters or damaged homes.
The storm was hitting the nation's southern land mass of Kyushu late Sunday.
The authorities in Kyushu urged residents to evacuate before rain intensifies.
The weather agency warned of heavy rain, landslides, strong winds and high waves.
In Japan evacuation orders are not mandatory and people often remain at home, only to become trapped later by rapidly rising water or sudden landslides.
Japan is now in typhoon season and is regularly hit by major storms during the summer and autumn.