The storm, which has been downgraded from typhoon status, has already prompted South Korea to begin the evacuation of tens of thousands camping at the World Scout Jamboree, which was earlier hit by a heatwave.
On Wednesday, about 16,000 households were without power as heavy rain pounded Japan’s southern island of Kyushu.
The Japan Meteorological Agency warned of torrential rain and the “surging” risk of “life-threatening mudslides and flooding” in the island’s Kagoshima region.
The US military’s Joint Typhoon Warning Center has designated the system a tropical storm with gusts of up to 130 kph (81 mph).
Japan Airlines on Wednesday cancelled 252 flights, affecting some 25,000 passengers, a spokeswoman told AFP. All Nippon Airways scrapped 96 flights, hitting over 10,000 people, a spokeswoman said.
The weather system, which killed at least two people in the Okinawa region last week, has already forced organisers to scale down and move inside Wednesday ceremonies marking the 78th anniversary of the atomic bombing of Nagasaki.
Japan’s “shinkansen” bullet train service was also halted in part of its southern route, while many other local commuter and express trains were cancelled, Kyushu Railway said in a statement.
In South Korea, where Khanun was expected to make landfall Thursday, nearly 80 flights at 10 airports and dozens of ferry services were suspended.
Seoul has raised its crisis alert level to its highest level, with the typhoon expected to have “a direct impact on the whole country” from Wednesday to Friday, said the interior ministry.
The presidential office was working around the clock on emergency typhoon watch, Yonhap news agency reported.
“We will do our best to respond to the typhoon, so that no human casualties occur, with thorough control and pre-emptive evacuation for the high-risk areas such as underground tunnels and riverbanks,” Interior Minister Lee Sang-min said Tuesday.
Another typhoon, Lan, was meanwhile forming in the Pacific, with gusts up to 108 kph and projected by the Japanese Meteorological Agency to move northwest towards the main island of Honshu in the coming days.