Typhoon Wipha is expected to make landfall right around the morning rush hour on Wednesday, bringing hurricane-force winds to the metropolitan area of 30 million people.
The centre of the storm was 860km southwest of Tokyo at 08:00, the Japan Meteorological Agency said on its website. It was moving north-northeast at 35km/h.
The storm had weakened as it headed north over the sea but was still packing sustained winds of about 140km/h with gusts as high as 194km/h, the agency said.
The agency issued warnings for Tokyo of heavy rain, flooding and gales, and advised people to be prepared to leave their homes quickly and to avoid unnecessary travel.
A spokesperson for the agency said the storm was a "once in a decade event" and the strongest cyclone to approach eastern Japan since October 2004.
That cyclone triggered floods and landslides that killed almost 100 people, forced thousands to evacuate their homes and caused billions of dollars in damage.
Four Japanese oil refining companies said they suspended marine berth shipments in eastern Japan as the typhoon approached but there was no impact on refining operations.
The affected facilities are Idemitsu Kosan's Chiba and Aichi refineries, JX Holdings's Negishi, Kashima and Sendai refineries, Fuji Oil's Sodegaura refinery and Cosmo Oil's Chiba refinery.
Japan Airlines cancelled 183 domestic flights on Tuesday and Wednesday, mostly from Tokyo's Haneda airport. Rival ANA halted 210 flights in Japan with three international flights also cancelled. The combined cancellations will affect 60 850 passengers, the airlines said.
East Japan Railway said it had cancelled 31 bullet trains going north and west from Tokyo.
Nissan Motor said it was cancelling the Wednesday morning shift at its Oppama and Yokohama plants south of Tokyo. Oppama makes the all-electric Leaf and other models.