Typhoon Phanfone, which was downgraded from an earlier status of a super typhoon, is moving at 20 kph (12 mph), the Japan Meteorological Agency said on Sunday.
It is expected to head north after hitting parts of Kyushu and Okinawa islands with heavy rain and wind. About 30 cm (12 inches) of rain and heavy wind are forecast for eastern Japan, including the Tokyo metropolitan area.
"My school has already decided not to have classes tomorrow," said Tomoko Kakinuma, a 20-year old college student in Tokyo.
On Sunday, Japanese airlines All Nippon Airways and Japan Airlines Co cancelled flights to several southern Japanese cities and Kyushu Electric Power Co said over 21,000 households were without power.
Nansei Sekiyu, a Japanese refiner wholly owned by Brazil's Petrobras, has suspended marine operations at its 100,000 barrels-per-day refinery in Okinawa due to the typhoon, but other operations are unaffected, a company spokesman said.
The approach of the typhoon also forced the suspension of search efforts on Mount Ontake in central Japan, where 12 people remain missing following a volcanic eruption that killed at least 51, Kyodo news agency said.