Up to 30 centimetres (12 inches) of snow was forecast for some parts of the country by Saturday morning, a week after the heaviest snowfall in decades left at least 11 people dead and more than 1,200 injured.
Tokyo had a thin covering by early Friday afternoon and the weather agency was warning it would continue into the night.
The agency also warned of heavy snow in western and central Japan as well as strong winds and high waves along coastal areas.
The storm caused delays on the "shinkansen" bullet train services.
Japan Airlines (JAL) said it had cancelled 77 flights for Friday and All Nippon Airways (ANA) grounded 40 flights across the nation. Jiji Press said 16,000 air passengers were affected.
Forecasters said the bad weather would continue into Saturday.
Last week, as much as 27 centimetres (10.6 inches) of snow was recorded in Tokyo, the capital's worst snowfall for 45 years.
While much of that snow had melted, the remains of larger piles as well as some slightly diminished snowmen were still in evidence across the city.