Despite the size of the city, Tokyo is a very safe place to study. Incidents of theft or violence are rare, but there are a few precautions advised by the local police.
Women – particularly when walking at night, it is worth staying on well lit major roads and/or in groups wherever possible. When riding bicycles, especially if you have just left a bank, do not put your handbag in the basket – there have been several “grab and run” motorcycle thieves. At night if walking alone it is advised to carry a small flashlight. Lock your apartment door. When looking for apartments/accommodation with a balcony, most Japanese women prefer an apartment that is not at ground level.
Rape and sexual harassment – Violent crime including rape is extremely low, though part of this may be due to under-reporting. At some stage or other there is the possibility of sexual harassment. Public transport can be very crowded in peak rush hour periods, and “women only” train carriages are available on the subways to enhance safety. (They also smell better).
Gay & Lesbian – There is an active gay and lesbian community in Shibuya and Shinjuku, and as a general rule Japan is a fairly tolerant and broad minded place, but some residents may take exception to overt displays of affection in public.
Hygiene and sanitation – The safety of food (in restaurants, at yataiya stalls during festivals etc) is of a high standard and safe. The tap water is safe to drink and does not need to be boiled before consumption.
Health & Insurance – The hospitals are of a high standard, but if you do not have insurance, can be very expensive. Student visa holders are automatically enrolled in the national health insurance scheme, which also includes dental care, but if you are entering Japan for a short term course using a tourist (tanki-taizai) visa, it is essential that you have either travel insurance or some other form of portable health insurance.