Domestic airlines including ANA, Japan Airlines and others cancelled a total of 100 flights due to the snow as of noon, according to the land ministry.
Parts of 31 highways were closed in central and eastern Japan, while 54 central Tokyo expressway exits were blocked, the ministry said.
Services on more than a dozen train routes in central and eastern Japan had suspended operations or were planning to do so, the land ministry said.
East Japan Railway, the country's biggest train operator, said a high-speed service between Tokyo and the northeastern prefecture of Yamagata would be suspended later on Friday.
Major delivery service firms including Yamato Transport and Sagawa Express said their delivery services may experience delays until Saturday.