The storm has moved east and is now covering all of the north of Japan's main island of Honshu and much of the northernmost island of Hokkaido, buffeting the region with strong winds caused by what meteorologists say is a severe low-pressure system.
On Sado island, on Honshu's northwest, gusts of up to 156 kilometres (97 miles) per hour were recorded.
The dead included a 96-year-old man who fell from the roof of a three-storey house during high winds and a 28-year-old woman who was hit by a falling tree while walking a dog.
The storm temporarily reduced electricity supplies to the Onagawa nuclear power plant, in Miyagi prefecture, halting the cooling system for a fuel pool, operator Tohoku-Electric Power Co. said.
Plant workers manually restarted the cooling system after about 20 minutes, it said. "There was no problem in the operation," a company spokesman added.
All reactors at the plant are currently idle.
The stormy weather also cut electricity supplies to 132,000 households in the northern Tohoku region as of mid-afternoon Wednesday, according to the utility.
Transport was widely disrupted on Tuesday as the storm moved through Japan, with about 600 domestic flights cancelled, affecting some 74,000 passengers.
On Wednesday 72 flights were grounded, stranding around 6,000 people.
Many commuter lines and some shinkansen bullet train services were also suspended because of the wind.