Eleven inches fell on the capital, the most in 45 years, meteorologists said.
More than 700 flights were suspended on Saturday and 300 were canceled.
Widespread power outages also occurred, as 15,400 households were without power, the Wall Street Journal reported.
The Japan Meteorological Agency said northeastern parts of the country will have more snowfall on Sunday.
The snow is also affecting voter turnout for Sunday's election for a new governor in Tokyo, the Journal reported.