Typhoon Halong slammed into western Japan on Sunday, making landfall on the main Honshu island as the weather agency issued its highest alert.
The strong typhoon hit Japan's largest and most populous island at around 10:00 am (0100 GMT) near the city of Ako on the southwest coast, the Japan Meteorological Agency said.
Packing winds of up to 162 kilometres per hour, the typhoon barrelled in to the smaller western island of Shikoku earlier Sunday, with huge waves battering the coast.
On Honshu, the weather agency maintained its highest warning -- meaning a threat to life and the risk of massive damage -- for Mie prefecture, some 300 kilometres (190 miles) west of Tokyo, warning that "unprecedented" torrential rain in the area could trigger massive landslides or major floods.
Storms and torrential rain earlier this week left one dead and 25 injured, Japan's public broadcaster NHK said.
Local authorities, mainly in western Japan, issued evacuation advisories to more than 1.6 million people in total, while a wide area on Shikoku island was submerged, NHK said.
At least 143 flights were to be cancelled on Sunday due to the typhoon, which came just as Japan began its annual "Obon" summer holiday, NHK said. On Saturday some 470 flights were grounded.
Typhoon Halong was moving north-northeast at 30 kilometres per hour, the weather agency said.
Halong comes a month after Typhoon Neoguri killed several people left a trail of destruction in southern Japan.
Last weekend a man drowned in a raging river, while more than half a million people were advised to evacuate as heavy rain from Typhoon Nakri lashed the country.