More than 740 flights were grounded as the weather agency issued a severe storm warning for the capital, while more than 40,000 households lost power.
As much as 22 centimetres (8.7 inches) of snow was recorded Saturday afternoon in Tokyo, topping 20 centimetres for the first time since 1994, the meteorological agency and news reports said.
Two female passengers, aged 88 and 90, died on Saturday in a car accident on their way to a nursing home in Ishikawa, central Japan, NHK said. Police suspect one of the cars skidded on the icy road and caused the head-on clash.
A man was also killed in Nagano as a train smashed into his car at a railroad crossing, the broadcaster said, adding that 3,200 other accidents occurred across the nation caused by vehicles skidding in the icy conditions.
Public broadcaster NHK said at least 494 people were injured in snow-related accidents across the nation.
Further snowfall is expected on Saturday night and early on Sunday in Tokyo, the weather agency said.
The agency issued a heavy snow warning for the capital, the first such warning for the capital in 13 years, calling on residents not to go out unless necessary.
The agency also warned of strong winds and high waves in eastern Japan as a rapidly developing low pressure front was heading toward eastern Japan, it said.
Japanese airline companies have cancelled 742 flights on Saturday due to heavy snow, NHK said, adding that more cancellations are expected on Sunday.
Airports in the western cities of Hiroshima and Kagawa were temporarily closed as operators were removing snow from the runways.
Television footage showed hundreds of passengers queuing for reimbursement or a change of flights at Tokyo's Haneda airport with departure boards indicating the cancellation of many flights.
Employees were hurriedly removing snow from the pavement in front of their shops and restaurants in Tokyo's bustling Ginza district.
Railway operators temporarily suspended services of Shinkansen bullet trains in western Japan, affecting more than 100,000 passengers, news reports said.
Some 43,800 households lost power in large areas of central and eastern Japan because of the heavy snow, the Yomiuri Shimbun reported.
Some sections of expressways mainly in central Japan were also closed due to the snow.
In Tokyo, several universities delayed the starting times of their entrance examinations for the new academic year starting in April.