Japan Airlines said it scrapped 42 flights, affecting 6,398 passengers, by early afternoon, all of them services to and from the northernmost island of Hokkaido.
Its main rival ANA also cancelled 14 flights, affecting 800 passengers, due to the rough weather in the north, and warned its customers of possible delays and more cancellations.
At the main airport of Hokkaido, passengers formed long lines to secure alternative flights.
Some prepared to see in 2025 in the departure lounge.
"It was great to see snow, but I didn't think I would be trapped here," one man trying to go home to Okinawa in the south told broadcaster HTB.
"I don't know what to do. I might have to stay at the airport tonight."
Hokkaido and communities along northern coastlines facing the Sea of Japan were experiencing strong winds and heavy snow Tuesday, according to the Japan Meteorological Agency.
More than 20 centimetres (7.9 inches) of snow has fallen in some areas of Hokkaido since Monday, most if it on Tuesday morning, the weather agency said, adding that snowfall was expected to continue on New Year's Day.
Japan's summer this year was the joint hottest on record -- equalling the level seen in 2023 -- as extreme heatwaves fuelled by climate change engulfed many parts of the globe.
Autumn was the warmest since records began 126 years ago, according to the national weather agency.
The famous snowcap of Mount Fuji was also absent for the longest recorded period this year, not appearing until early November, compared with the average of early October.
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