Heavy snow and severe weather has struck Tokyo and other areas across Japan, leaving two dead and around 90 injured, reports say.

More than 600 flights were grounded as the weather agency issued a severe storm warning for the capital.

As much as 12 centimetres of snow was recorded on Saturday afternoon in Tokyo, with a rapidly developing low pressure front heading toward eastern Japan, the meteorological agency said.

Public broadcaster NHK said at least 89 people were injured in snow-related accidents only in eastern Japan, including 17 serious injuries.

It also 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. Police suspect one of the cars skidded on the icy road and caused the head-on clash.

Further snowfall is expected  early Sunday in Tokyo, with up to 20 centimetres of snow expected, the weather agency said.

The agency issued a heavy snow warning for Tokyo, 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.

Japanese airline companies have cancelled at least 615 flights on Saturday due to heavy snow, NHK said.

Railway operators temporarily suspended services of Shinkansen bullet trains in western Japan, NHK said.

Some sections of expressways mainly in central Japan were also closed due to the snow.