Some two centimeters (four-fifths of an inch) of snow accumulated in downtown Tokyo, the first time since 1998 that more than one centimeter of snow covered the Japanese capital, according to the meteorological agency.
All Nippon Airways said it had cancelled 38 domestic flights out of Haneda airport in the metropolis. Its main competitor Japan Airlines said it had called off several flights.
Shinkansen bullet trains were running at lower speeds near Tokyo, leading to delays, as the snow turned into rain and slush by late morning.
Sections of expressways were also temporarily closed as a precaution.
No damage or injuries were reported.