Health and Safety

Stay healthy
Japan is a country obsessed with cleanliness and health hazards are few and far between. Tap water is potable everywhere and food hygiene standards are very high. There are no communicable diseases of significance, as despite the name, Japanese encephalitis has been all but eradicated.
Some Japanese public toilets do not have toilet paper, although there are often vending machines nearby that sell some at token prices. Do as the Japanese do and use the tissue packets handed out free by advertisers at major train stations.
Though it's common sense for people who have lived in urban areas, many newcomers to Tokyo or Osaka are unfamiliar with life in an extremely congested metropolis, where almost everything they touch has been touched by hundreds of other people that same day. When newcomers to large Japanese cities don't take basic precautions, they may be more susceptible to ordinary illnesses like the common cold. As in any urban area, when in a large Japanese city like Tokyo or Osaka, wash your hands with soap and water as often as possible, especially after travelling on public transportation and before meals.
Be sure to bring a small umbrella for the frequent rainy days. Don't rely too much on the weather forecasts, especially from a day or two ago. Then again, if caught without, you can always go into the nearest convenience store and pick one up for ¥500.
Japan has its share of dirty areas. In cities, because of the sheer magnitude of traffic, the streets and curbs are just as dirty as anywhere. The obsession of cleanliness and removing shoes before entering someone's home makes sense because of the conditions of the outer world.
If you do become ill with a cold or other sickness, purchase a mouth covering, a cloth surgical mask. You will find that people frequently wear these out on trains and on the job. This filters your sneezing and coughing so you do not transmit to others.
Passive smoking is a major health hazard in nearly all Japanese restaurants and public areas; this includes Multi-national food chains as well as local eateries. Non-smoking areas are not often provided and are sometimes substandard if they are.

Stay safe

Japan is probably one of the safest countries in the world, with crime rates significantly lower than that of most Western countries.

Crime and scams

Police and the law
Police in Japan may and do detain people up to 23 days before a prosecutor formally files charges, a privilege unrivalled in the Western world (except during terrorism investigations). During this period, you may be subjected to non-stop interrogation. You can hire a lawyer, but only if somebody outside pays his/her fees in advance. Your lawyer is not allowed to be present during interrogations. Insist on an interpreter and consular access, and do not fingerprint (Japanese equivalent of signing) anything, especially if you do not fully understand what you sign: if you sign a confession, you will be found guilty at trial.
So how to avoid this unpleasant fate? By far the most common pattern of how foreign tourists end up staring at the cold, yellow walls of a Japanese detention cell is getting drunk first and into a fight, or even near one, later. Standard police procedure is to detain everybody first and sort out things later. If anybody accuses you of anything even on the flimsiest grounds, you may be looking at an unpleasant extension to your vacation.
Japan is exotic and mysterious; what seems strange and even appealing to you during daytime, can get obnoxious and annoying to you at night, especially with some booze running through your veins, so control your temper and alcohol level. Police patrol party areas heavily at night and they will be more than willing to "rescue" a fellow Japanese from a violent foreigner.
Street crime is extremely rare, even late at night. Of course, little crime does not mean no crime, and is not an excuse to ditch your common sense. Women travelling alone should take care as they would in their home countries and should never hitchhike alone. Pickpocketing does sometimes happen - if you take your usual precautions in crowded places such as trains and at Narita Airport you should be fine. Women on crowded rush-hour trains should be aware of existence of chikan (痴漢), or molesters. A lot of heavy drinking goes on in the evenings and occasionally drunks may be a nuisance, although alcohol-related violence is extremely rare.
The infamous yakuza (ヤクザ) or Japanese gangs have earned a partly undeserved reputation of being a bunch of violent, psychopathic criminals due to their portrayal in various films. However, in reality, even though they are largely associated with the vice trades, they rarely target the average person on the street. Just do not find trouble with them, and they would not bother you.
Note that drug laws in Japan are stricter than those in many Western countries. Possession of even personal-use quantities can land you a prison sentence of several years, and Japanese law does not distinguish between marijuana and hard drugs.
Red-light districts in large cities can be seedy but are rarely dangerous for visitors, however some smaller backstreet bars have been known to lay down exorbitant cover charges or drink prices. In some extreme cases, foreigners have reported being drugged at such establishments, then charged for as much as ¥700,000, or close to US$7000, for drinks that they do not remember ordering (notably in the Roppongi and Kabuki-cho districts of Tokyo). If you choose to visit an establishment in one of these locales, be sure to note the price and address before entering.
Police boxes (交番 kōban) can be found on every other street corner. The police are generally helpful (but often speak little English), so ask if you get lost or have any trouble. They usually have detailed map from the area around telling not only the difficult-to-understand numbering system but names of office or public buildings or other places which can help to find your way. Also, if you carry travel insurance, report any thefts or lost items at the koban. They have forms in English and Japanese, often referred to as the "Blue Form". For lost items, even cash, filling out this form is not wasted effort, as Japanese people will very often take lost items, even a wallet full of cash, to the koban. If you happen to find such an item, don't hesitate to take it to the koban. If the item is not claimed within six months, it is yours. If it is claimed, you may be due a reward of 5-15%.
Japan has two emergency numbers. To call the police in an emergency, dial 110 (百十番 hyakutoban). To call for an ambulance or fire truck, dial 119 (a reversal of the US 911). In Tokyo, the police have an English help line (03-3501-0110), available Monday through Friday except on holidays from 8:30 AM - 5:15 PM.