At least three people have died in heavy snow that has blanketed swathes of Japan with up to two metres lying in some places and more forecast.

Two elderly women were killed on the northernmost island of Hokkaido, Kyodo News reported, with one hit by a snow-plough and another buried when a warehouse collapsed under the weight of fallen snow.

Police said a man died in a traffic accident on snow-bound roads in Hiroshima on Thursday.

There was also widespread disruption to travel, with around 100 domestic flights cancelled, adding to the 450 that were grounded on Wednesday, including some international routes, officials and media said.

Reports said the famous bullet train network was also struggling to stick to its timetables.

The mountain town of Tsunan, near the Sea of Japan (East Sea) coast, was smothered in 185cm of snow, with parts of Hokkaido getting as much as 70cm in 24 hours, the Japan Meteorological Agency said.

The snow is accompanied by strong gusting winds of up to 140km/h, which is causing tidal surges and sparking warnings to stay away from the water's edge.

Forecasters said a powerful low pressure system off the eastern coast of Hokkaido was bringing much of the misery, and warned there was more to come.

Parts of northern Honshu could expect up to 80cm of snow by breakfast time on Friday, the JMA said.