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Smoking is prohibited in most public places. In some places it is illegal to smoke anywhere outside. It varies from region to region but general smoking outside official areas in frowned upon and can lead to you being fined
The airports in Japan are some of the best places to travel to/through/from for the travelling smoker.
The Japanese Bullet Trains (Shinkansen) have smoking rooms and for the smoking tourist, the Green Car Pass is the greatest travel on earth for a smoker. Update from Charles, March 2019