Japan's Meteorological Agency (JMA) has confirmed Typhoon Hagibis has reached Kawasaki, a western part of greater Tokyo.
Hours after the typhoon made landfall just before 7:00pm local time on Saturday, the agency said it was advancing north-northwestward with maximum sustained winds of 144 kilometres per hour, travelling northward at a speed of 40 kph.
Around the same time as the typhoon was making landfall, a moderately strong 5.7 magnitude earthquake struck offshore in the country's south-east.
The earthquake was felt across Tokyo and Chiba.
Four people remained unaccounted for in Gunma and Shizuoka prefectures.
Two workers trying to manage a rising river were swept away in flood waters in Shizuoka.
One was rescued after clinging to a tree, the other remains missing and a search is underway.
In Tomioka City in Guma, mudslides flowed into six houses prompting a rapid search and rescue operation.
Six people were rescued, but three people remain missing.
While no tsunami warning has been issued, it was feared the earthquake would loosen already inundated sand, leading to a higher potential for deadly landslides.
Officials from the JMA have said it was likely serious disasters have already occurred.
© Provided by Australian Broadcasting CorporationSocial media users posted striking images of eerie purple skies as one of the most powerful typhoons in 60 years swirled towards Japan. (Twitter: @sengdayritt)
The organisation has issued further emergency heavy rain warnings for Fukushima, Miyagi, Ibaraki, Tochigi and Niigata prefectures.
These are also at the highest level of warning and indicate that a serious disaster may have already occurred.
Residents have been told to take immediate actions to protect their lives.
The warning to the additional five prefectures brings the total to 12 prefectures.
The earthquake and arrival of Typhoon Hagibis come after the weather agency issued its highest alert level to several prefectures, including some in Tokyo, in anticipation of the typhoon's arrival.
Major disaster possibility
The level five warnings alerted locals to the possibility that Typhoon Hagibis could bring unprecedented rainfall with the possibility of major disaster, including flooding and landslides.
Millions of people across Japan were advised to evacuate their homes due to fears of flooding as the super typhoon approached - which experts have warned could be more powerful and destructive than the 1958 storm that left 1,269 people dead.
Overnight, residents posted surreal images of the sky transforming into electric shades of purple and pink. One Twitter user commented that the "beautiful scene" disguised a "big catastrophe".
The vivid purple tint is the result of a weather phenomenon called "scattering", which happens when the molecules and small particles in the atmosphere influence the direction of the light, causing the light to scatter.
Heavy storms and rain tend to wash away larger particles - which absorb more light and scatter wavelengths more evenly, resulting in muted hues - out of the air, making the colours of the sky more vivid.
Typhoon Hagibis, which means "speed" in the Philippine language Tagalog, comes just a month after one of the strongest typhoons to hit the country in recent years destroyed or damaged 30,000 houses and caused extensive power outages.
Maximum gusts of 216 kilometres per hour were forecast by the time Hagibis crashes into land, according to the JMA.
According to local emergency workers, one person had died and five people were injured when early on Saturday the storm's outer bands began lashing Chiba - a prefecture east of Tokyo that was hit hard by typhoon Faxai a month ago.
"A 49-year-old man was found in a toppled mini truck and sent to hospital but was confirmed dead," Hiroki Yashiro, a spokesman at Ichihara Fire Department, in Chiba, said on Saturday morning.
Strong winds blew roofs off several houses and upturned cars, while violent waves crashed into the coastline.
Pictures: Typhoon Hagibis
By midday, 1.64 million people in the affected area were under non-mandatory evacuation orders, with authorities urging the elderly, disabled and those with children to leave early.
More than 1,600 flights around the country have been grounded and many of the country's famous Shinkansen bullet train services have been suspended.
Department stores and shops were closed and streets were empty in central Tokyo while factories and subway systems all around Honshu have also been shut down as a precaution.
Images posted to Twitter showed panicked shoppers clearing out supermarket shelves ahead of the storm, while Japanese Formula One Grand Prix organisers cancelled all practice and qualifying sessions scheduled for Saturday.
Two matches of the Rugby World Cup due to be played on Saturday were also cancelled.
Storm surges are expected along the Pacific coast of Honshu on Saturday and Sunday, along with torrential rain, raising the risk of floods and landslides.
According to the JMA, the predicted rainfall amounts would be in line with those deposited by Typhoon Ida - known as the "Kanogawa Typhoon" in Japanese - in September 1958, which left more than 1,200 people dead or missing across Japan.