Snow began falling Friday morning in Tokyo and piled up to 26 centimetres by early Saturday, a week after the heaviest snowfall in decades left at least 11 people dead and more than 1,200 injured across the country.
A driver was killed on Friday in a crash involving his car and a truck on an icy road in Shiga, central Japan, while a farmer died after a tractor overturned on a snow-covered road in southwestern Oita.
In a separate snow-related accident, a driver was killed and three others injured on an expressway in central Shizuoka.
The public broadcaster NHK said some 850 people, including one in a coma, have been injured in snow-related accidents across the country since snow hit western Japan late Thursday.
Drivers were struggling to move their cars in the capital's residential district of Setagaya, while snow started melting and flooding some roads in downtown Tokyo.
Television footage showed hundreds of passengers resting on benches and floors under blankets at Haneda airport as public transport services were suspended due to heavy show.
At least 628 flights, mostly on domestic routes, were cancelled on Saturday at Haneda and other airports in eastern Japan, NHK said, a day after more than 260 flights were grounded due to heavy snow.
Two commuter trains collided at Motosumiyoshi station in Tokyo early Saturday leaving 19 passengers injured. The accident occurred as train services were disrupted due to the storm but it was not immediately clear if the collision was directly related to the bad weather.
The storm also caused delays and suspensions on the Shinkansen bullet train services and the closure of a number of highways.
About 187,000 households lost power mainly in eastern Japan due to snow and strong winds, NHK said.
The meteorological agency continued warning of heavy snow in eastern Japan as well as strong winds and high waves along coastal areas, which may cause snowslides.