Hagibis made landfall in the Izu Peninsula shortly before 7 pm (2100 AEDT), Japan Meteorological Agency said.

One person was found dead in an overturned vehicle in the city of Ichihara, east of Tokyo, and five others were injured when a tornado touched down in the area early Saturday, destroying one house and blowing away the roofs of several houses, local media reported.

Three people are unaccounted for in the city of Tomioka, about 120 kilometres north-west of Tokyo, after a landslide hit six houses there, broadcaster NHK reported. Six residents were rescued.

One person was missing in the central city of Gotemba after he was swept away in a drain, the Kyodo News agency reported.

More than 1 million people were ordered to evacuate their homes in eastern and central Japan as the storm brought heavy rains and powerful winds, inundating residential areas in the regions.

Meteorologists issued an emergency rain warning to seven prefectures, including Tokyo and Shizuoka, as they warned of mudslides, flooding and swollen rivers.

At a news conference, Yasushi Kajihara, who heads the forecast division at the Meteorological Agency, warned of "rainfall of the kind that you have never experienced before" in those prefectures.

Since Thursday, Hakone Town, west of Tokyo, had received more than 800 millimetres of rain and the city of Izu more than 700 mm, Kyodo reported.

About 122,000 households lost electricity in the Kanto region and Shizuoka prefecture, Tokyo Electric Power said.

The storm caused more than 1,660 flights to be cancelled, according to broadcaster NHK, while many train services, including high-speed bullet train services, were halted.

As of 7 pm local time, Hagibis was travelling north-north-east at 35 km/h with maximum sustained winds of 144 km/h and gusts of 216 km/h, according to the Japan Meteorological Agency.

The storm is expected to dump 400 mm of rain in the Hokuriku region, 300 mm in north-eastern Japan and 250 mm in the regions of Kanto and Koshin by Sunday evening, the agency said.

Hagibis is comparable to the 1958 typhoon that hit eastern and central Japan, killing more than 1,200 people, the agency said.

Two rugby World Cup games scheduled for Saturday were cancelled due to the expected impact of Hagibis, while the typhoon also affected the Formula 1 Japanese Grand Prix this weekend at Suzuka.

Qualifying has been moved from Saturday to Sunday, F1 officials said, and all events were cancelled on Saturday at the Suzuka Circuit.

Hagibis comes one month after Typhoon Faxai battered eastern Japan, including Tokyo, leaving one dead and about 130 injured and causing massive power outages.

Australian Associated Press