Heavy snow that blanketed eastern Japan over the holiday weekend left one man dead and 900 others injured, as Tokyo commuters Tuesday took to the slippery streets.

A low-pressure system, dubbed a "bomb cyclone" by local press, dumped eight centimetres (three inches) of snow in nine hours, the heaviest snowfall in the region since January 2006, the Japan Meteorological Agency said.

It left 13 centimetres of snow in neighbouring Yokohama, while mountainous areas around Tokyo saw up to 30 centimetres.

A 71-year-old man in Shiojiri city, Nagano prefecture, died after falling into an open drain as he cleared snow around his house, a fire service spokesman said.

National broadcaster NHK said at least 891 injuries had been recorded in Tokyo and the area around it, many of them elderly people who had slipped on snow-covered streets or motorists involved in accidents.

The operator of the Tokyo Skytree, a 634-metre (2,080-foot) tower in the capital that opened last year, said security guards were patrolling the base to keep people away from possible ice falls.

"We haven't received any reports of damage or injury from falling blocks of snow," said spokeswoman Ayumi Kimura, adding around 60 guards were in the area Tuesday.

"We have confirmed snow has fallen in tiny chunks. But there has been a limited amount of snow that has fallen on the tower."

Major train services resumed operations in Tokyo, although many sections of road remained closed while crews cleared frozen snow.

All Nippon Airways and Japan Airlines cancelled a combined total of 37 domestic flights while dozens of other flights experienced delays.

International operations were not severely affected by the snow, the airlines said.

On Monday, Japanese airlines cancelled more than 460 domestic flights, mainly to or from Tokyo's Haneda airport, where runways were temporarily closed as workers removed snow.

Around 3,400 people spent the night at Tokyo's Narita airport on Monday, a spokesman said after train services running to the outlying facility were suspended.

They returned to normal on Tuesday, he added.