More than 500 houses in several prefectures were flooded due to the typhoon and heavy rain, according to public broadcaster NHK, with about 130,000 households urged to seek shelter.
"Water kept gushing into the house no matter how hard we tried to pour it out. We kept shoving out water all night," said a woman in northern Yamagata Prefecture, where humid air brought by the typhoon caused huge downpours.A Moderate Resolution Imaging Spectroradiometer (MODIS) image from NASA's Terra satellite shows Typhoon Neoguri in the Pacific Ocean approaching Japan's main islands on its northward journey (Reuters photo)
"Officials warned over the risk of flooding and landslides as powerful winds and torrential rain batter the archipelago nation, with local authorities urging half a million people to seek shelter in Okinawa earlier in the week.
Neoguri hit the mainland on Thursday morning near Akune City on the southern main island of Kyushu, which is home to 13 million people and lies next to the country's biggest island of Honshu where major cities including Tokyo and Osaka are located.
The typhoon had crossed Kyushu by late morning and was forecast to make a landfall on Honshu by Friday.
The storm's ferocity slowed somewhat overnight, now packing gusts of up to 126 kilometres (80 miles) per hour as it moved east at 25 kilometres per hour.
Nearly 50 people have been injured in the wake of the storm, officials and reports said, while as many as five deaths have been directly or indirectly linked to the typhoon.