The typhoon, which is projected to reach South Korea's southern coast on Thursday, is lingering in the Pacific Ocean, about 200 km (124 miles) south of Japan's third-largest island Kyushu, Japan Meteorological Agency (JMA) said.
Thunderstorms, with precipitation of up to 400 mm (16 inches), were expected to lash areas of Kyushu and neighbouring Shikoku island in the next 24 hours, JMA said. Areas as far north as Osaka and Nagoya are also likely to be affected.
"Due to the slow movement of the typhoon and its prolonged impact, total rainfall may greatly exceed the normal monthly rainfall for August," the JMA added. Khanun is moving at less than 10 km per hour (6 mph).
Trains, flights and ferries were cancelled for the next couple of days.
The city of Nagasaki also relocated a venue to commemorate the 78th anniversary of the U.S. atomic bombing on Wednesday to an indoor convention centre from a park.
In Kyushu's Kagoshima prefecture, about 950 km (590 miles) southwest of Tokyo, 60,000 households were advised to evacuate, Japan's Fire and Disaster Management Agency said. In the western part of the country's largest Honshu island, Mazda Motor said it would suspend production at its two plants in Hiroshima and Yamaguchi.
Khanun rolled into Japan's southernmost Okinawa last week, causing blackouts in more than 200,000 buildings. The storm has since gradually lost its strength but still packs winds of up to 144 kph (40 mph).
Airlines, including Japan Airlines and All Nippon Airways, cancelled 222 flights on Tuesday, bringing the total number of flights disrupted by Khanun since last week to 2,715, according to a transportation ministry tally.
South Korea on Tuesday started evacuating thousands of participants at the World Scout Jamboree ahead of Khanun's approach.
Another typhoon has also emerged in the Pacific, the JMA said. Typhoon Lan, with winds of up to 180 kph is expected to reach central Japan on Sunday.
(Reporting by Satoshi Sugiyama and Kantaro Komiya; Editing by Gerry Doyle and Miral Fahmy)
By Satoshi Sugiyama and Kantaro Komiya