Tokyo has been hit by a rare snowstorm with reports of up to 23 centimetres in some suburbs.

The threat of snow prompted the country's Meteorological Agency to issue its first warnings for heavy snow since February 2014.

The snow, which began on Sunday night and continued through Monday, was nowhere near as disruptive as 2014's snow, which resulted in four days of turmoil.

Nevertheless, an emergency announcement was made by the transport ministry on Sunday advising people to stay at home unless absolutely necessary.

The Yurikamome Line, which traverses Tokyo Bay, came to a halt after a train failed to negotiate the incline.

Japan Airlines cancelled more than 120 flights on Monday from Haneda airport, affecting around 15,000 passengers.

On Monday evening, 50 cars were stranded on the Rainbow Bridge over Tokyo Bay due to heavy snow and a series of accidents.

Snow is rare in Tokyo because it lies on the eastern side of Honshu and it is sheltered from weather systems approaching from the north and west by the Japanese Alps.

The city tends to be more vulnerable to systems approaching from the much warmer southwest.

For northern and western Japan, snow is heavier and more widespread as cold air sweeps in unhindered from the cold winter steppes of Mongolia, Siberia and Manchuria.

More heavy snow is expected across Hokkaido, and western Honshu through Wednesday, with up to half a metre of snow in some areas. Tokyo should continue to miss the worst of the snow as the southwesterly winds will help temperatures reach around 10 degrees Celsius.