The eye of Typhoon Hagibis made landfall shortly before 1000 GMT in Izu Peninsula, southwest of Tokyo, Japan's Meteorological Agency said.
Powerful Typhoon Hagibis barrelled through Japan on Saturday, killing at 16 people and lashing large parts of the country with "unprecedented" rain that caused floods, landslides and emergency disaster warnings.
Around 7.3 million people were given non-compulsory evacuation orders, and more than 149 were injured, while 15 people were reported missing as flooding hit many towns and cities.
Typhoon Hagibis has left seven dead and 15 missing, Japan's chief government spokesman Yoshihide Suga said.
He says damage to housing from the flooding is extensive but promised recovery is on its way. Some 376,000 homes are without electricity, and 14,000 homes lack running water.
Boats as well as helicopters are being deployed to the flooded areas, while rescue crew are digging through dirt in other areas to try to get people out from homes buried by landslides.
Even before making landfall, Hagibis wreaked havoc on two major sporting events, the Rugby World Cup – where two matches were cancelled for the first time in its 32-year history – and the Japanese Grand Prix, which postponed qualifying.
Transport disruption was also widespread, with authorities halting suburban trains in Tokyo throughout most of Saturday, suspending several bullet train lines and cancelling all flights in and out of the capital's two main airports.
Hagibis smashed into the main Japanese island of Honshu around 1000 GMT as one of the most violent typhoons in recent years, with wind gusts of up to 216 kilometres per hour.
Well before making landfall, the outer bands of the storm claimed their first victim, a driver whose van was flipped over in the strong gusts.
The second confirmed death was a man in his 60s killed in a landslide north of Tokyo.
Another man in his 60s was also confirmed dead after he was pulled from his flooded home in Kawasaki city, near Tokyo.
"The house was two to three metres (yards) under water and the team rescued the man from there" but he was confirmed dead later, local fire department official Kiichi Hayakawa told AFP.
Public broadcaster NHK also said a woman near Tokyo was feared dead after a landslide.
The typhoon even caused a tornado in Chiba, east of Tokyo, an area badly damaged by Typhoon Faxai last month.
The twister destroyed one house and damaged several others. Five people – including a three-year-old boy – were taken to hospital with minor injuries.
They were among at least 96 people injured in the typhoon, with at least 14 still unaccounted for, Japanese media reported.
As Hagibis drenched Tokyo and the surrounding areas with torrential rain, the Japanese Meteorological Agency issued its highest-level emergency warning, advising people to seek shelter for protection.
"Unprecedented heavy rain has been seen in cities, towns and villages for which the emergency warning was issued," JMA forecaster Yasushi Kajiwara told reporters.
"It is important to take action that can help save your lives."
Tens of thousands heeded the advice to huddle in emergency shelters although nerves were further jangled when a 5.7-magnitude earthquake jolted Tokyo and surrounding areas early Saturday evening.
"I evacuated because my roof was ripped off by the other typhoon and rain came in. I'm so worried about my house," a 93-year-old man told public broadcaster NHK at a shelter in Tateyama, in Chiba, east of Tokyo.
In Yokohama, outside of Tokyo, others hunkered down in their homes despite the storm.
"I'm 77 and I've never seen anything like this," Hidetsugu Nishimura told AFP.
"We can hear an infernal din from the rain and the wind, and a fragment of the roof has gone. For an hour, the house was shaking from wind and rain."
Several rivers broke their banks, including the Tamagawa that flows through a residential area of Tokyo.
Among the missing were three people swept away in their car after a bridge over the River Chikuma broke, local official Masataka Tomi told AFP.
There were fears of more potential flooding after officials opened sluice gates at several dams, warning residents downstream to evacuate if possible.
Nearly half a million households in the greater Tokyo area lost power at some stage during the storm.
Beleaguered Rugby World Cup officials warned that at least one other fixture cancellation was possible on Sunday after the scrapping of two matches scheduled for Saturday.
Organisers warned people not to travel to the northern town of Kamaishi, an area devastated by a 2011 tsunami where a match between Namibia and Canada was due to take place.
All eyes are on the crunch Pool A match in Yokohama between hosts Japan and Scotland that will determine which of the two teams progresses to the quarter-finals.
Organisers have said they will assess venue infrastructure before deciding whether to play the match, amid threats from Scotland of legal action if they are eliminated without getting a game.
World Rugby called the Scottish comments "disappointing."