A news story about the murder of a young (female) British language instructor in Tokyo by a Japanese man whose home she presumably visited to conduct a private language lesson is making the rounds of all the news sites and Japan blogs. If you haven't read the story, you can read a bit of it on Japan Probe as well as follow their links to related articles.
I generally try to refrain from commenting on news stories, particularly when they're as well-covered as this one has been and will continue to be. However, this terrible story hits a bit closer to home for me because I'm female, teach in my home, and have been followed around and harassed by creepy Japanese men before, though fortunately never stalked as the victim was. One even grabbed my ass twice as I was riding down an escalator early on in my stay in Japan (when I was young enough to be worth a pervert's attention, I guess).
This story isn't really about being a foreigner in Japan though. It's really more about the half truth that Japan is a safe country and the reality of being a woman of any nationality in Japan. While Japan is safer than some other countries, that doesn't mean that it is "safe". This is much more so the case for women than men since violence against women is not treated as a serious problem in Japan relative to other developed countries.
Since Japan has all the trappings of a refined, civilized, and polite society where people have better control of their emotions and reactions than people back home, it's easy to believe that people treat each other well most of the time and to conclude the gentle demeanor you witness in public continues in private. The truth is that domestic violence is under-reported and often ignored by the police when it is reported. When rapes are reported, the woman is often held partially or even fully responsible for "allowing" the crime to happen or even "facilitating" it by showing what the police feel is questionable judgment.
Underestimating the potential for violence and brushing off the nuisance of unwanted attention is an easy mistake to make because many Japanese strangers can come across as weak, ingratiating, or amusing in their attentions toward foreign people for the most part. They rarely come across as especially intimidating. If you're an English teacher, it becomes even easier when you hear students telling you day-in and day-out that they don't want to live abroad because Japan is a "safety country" and other places are dangerous.
Japan's safety is a half truth that needs to be let go of. There are violent crimes, petty thefts, and a lot of shady dealings. The statistics you hear about crime in Japan are not representative of reality for a variety of reasons and should not be trusted. Many small crimes go unreported because the Japanese don't want to rock the boat or get someone in trouble because there's a social price to pay for being a petty criminal. The police often adopt a cooperative attitude with organized crime whereby they allow them to go about their business as long as they don't disrupt the orderly flow of society in any appreciable way. There are also a lot of back-door dealings when crimes are committed where apologies are made and money changes hands to keep crimes from being handed over to the criminal justice system.
I abandoned the idea that Japan is safe a long time ago. I always lock my front door (and chain it) and I never open the door to strangers or unexpected visitors. I also approach the front door with my key in hand so I don't have to fumble or delay in getting in. While I do have students come to my home, all but one are women and the lone male is 65 years old and had been attending lessons with another teacher for 3 years before being referred to me.
The fact that my 20-year-old apartment came pre-built with full-size metal shutters that lock over the door-size glass windows on one side of the building and bars over the windows on the other is an indication that the Japanese don't necessarily embrace the idea that their country is safe either. Otherwise, why would such precautions be taken to keep intruders out?