The spring storm swept across Japan's main island of Honshu, with typhoon-strength winds of more than 89 miles an hour.
The country's meteorological office said the storm had left the region, but it urged caution as strong winds would persist in parts of northern Japan.
Two people were killed in separate warehouse collapses in Toyama in the north, and Kagawa in the south. Police reported a further two deaths overnight: an elderly man who fell off a roof in Iwate and a woman crushed by a fallen tree in nearby Miyagi.
Officials said hundreds more had been injured across the country.
The storm brought commuter train services to a halt and grounded more than 500 flights in and around Tokyo. Train services returned to normal on Wednesday but about 70 more flights were cancelled.
The cooling of spent fuel storage pools at two nuclear power plants in northern Japan halted temporarily when pumps stopped because of a power failure but resumed after about 30 minutes without affecting safety, according to their operator, Tohoku Electric Power Co.
The Fukushima Daiichi nuclear power plant, which suffered meltdowns at three reactors after last year's tsunami, was unaffected by the storm.
