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Japan is not as safe for women travellers as it is for men. The primary dangers faced by women travellers to Japan are of a sexual nature: sexual harassment, molestation and rape.
Although some expats will assure you that it's safe to walk the streets of any Japanese city alone at night, ignore this nonsense and follow your common sense: keep to streets with heavier foot traffic, stay in groups etc. Western-looking women who are alone on foot are easy targets for verbal harassment, or worse, by passing male pedestrians, cyclists and motorists. Walking solo along roads in remote rural areas (even during broad daylight), and hitchhiking are definitely advised against. The risks simply aren't worth it.
Jam-packed trains or buses during rush hour, or late-hour services heaving with the inebriated masses, can bring out the worst in some men. If possible, ride in the women-only train carriages that have recently been introduced. Some Japanese men engage in the all-too-common handshake scam, where a friendly man pretends to want to shake your hand Western-style, then fondles your breast at the same time. When in doubt, refuse to shake hands and bow instead. Although statistics show low rates of violent crimes against women, many Japanese women's organisations and media attribute this to under-reporting.
