Warnings had been issued across South Korea, with over 330 flights cancelled and more than 10,000 people evacuated.
Khanun was over the ocean and passing between Kyushu, Japan's southwestern main island some 860km (530 miles) from Tokyo, and the Korean Peninsula. It was picking up speed slightly and moving north at 20 kph (12.5 mph)
Outdoor activities were halted for scouts visiting South Korea for the World Scout Jamboree. About 37,000 scouts were evacuated from their campsite in southwestern South Korea on Tuesday.
Fed by humid air from Khanun, heavy rains kept pounding a wide swathe of western Japan, where some areas have been hit by well over a normal August's worth of rain in the past week. One town had recorded 985 millimeters (39 inches) as of Thursday morning.
Attention was also turning to Typhoon Lan, which passed near the Ogasawara Islands, about 1,000km (600 miles) south of Tokyo, late on Wednesday and was heading north northwest at 15 kph (9.3 mph).
Though uncertainties remained about the storm's path, the Japan Meteorological Agency (JMA) said it could affect the Tokyo area towards the end of the weekend.
The bad weather is striking in the middle of Obon, Japan's main summer holiday period in which thousands leave big cities to return to their home towns elsewhere in the nation.
(Reporting by Elaine Lies and Hyunsu Yim; Editing by Lincoln Feast)
