Typhoon Goni damaged buildings, tossed around cars and flooded streets in southwestern Japan on Tuesday before heading out to the Sea of Japan.
No deaths were reported, but at least 26 people were injured, according to Japan's Fire and Disaster Management Agency.
The same storm struck the Philippines earlier, where the death toll rose to 21 with 15 still missing as search and rescue efforts continued.
Typhoon Goni made landfall after daybreak Tuesday on Japan's southernmost main island of Kyushu, bringing fierce winds and heavy rain to much of western Japan.
Flights to and from Kyushu were canceled, and train and bus service suspended. Japanese television showed uprooted trees, downed power lines and sheared-off building walls and roofs. More than 470,000 households temporarily lost power, Kyodo News service reported.
After sweeping across the island, Goni was heading north with maximum sustained winds of 126 kph (78 mph) and gusts to 180 kph (112 mph), the Japan Meteorological Agency said.
In the northern Philippines last weekend, the typhoon triggered landslides and flash floods. A deadly mudslide in the mountainous province of Benguet buried gold miners in three work camps.