Typhoon Vongfong was downgraded to a tropical storm as it made landfall on the island of Kyushu, but the powerful storm still picked up speed as it moved north along the Japanese main island of Honshu late on Monday.
Heavy rain had already spread to Japan's main islands as the storm continued its path across the country.
Japan's Meteorological Agency said Vongfong still had winds of up to 160 kilometers per hour (100 mph) Monday after being downgraded to a tropical storm.
Forecasters expect it to hit the Tokyo area by early Tuesday.
Authorities warned of landslides and flash floods in areas where the typhoon is forecast to traverse.
The typhoon also paralyzed traffic, stranding tens of thousands of people traveling around the country at the end of a three-day national holiday.
Airlines have canceled more than 500 flights, while West Japan Railway said it planned to suspend all local services in the western region of Kansai later Monday.
The storm peaked with winds of 234 kilometers per hour (145 mph) Saturday, and has damaged homes and caused transportation delays as it crossed over Japan's southern Islands.
The storm has injured at least 56 people. Authorities issued evacuation warnings and advisories across 13 prefectures, bringing the total number of those called to evacuate up to more than 1 million people as of 6 p.m. local time (1000 GMT), according to Japan's Fire and Disaster Management Agency.
On Sunday, Vongfong brought high waves to coastal cities in east China Zhejiang province, inundating ports and streets in Zhoushan City, raising the water level to 50 centimeters in less than two hours.
Vongfong is the second typhoon to hit Japan in the past week, after Typhoon Phanfone leaving 11 people dead or missing, including three U.S. servicemen based in Okinawa.
Due to the latest storm, the search was suspended for the bodies of at least seven hikers believed to remain on the still-smouldering Mount Ontake, where 56 bodies have already been retrieved.
The volcano was packed with walkers when it burst angrily to life on September 27, with many there to witness the spectacular autumn foliage.
Some material for this report came from Reuters, AFP and AP.