If you come from a western country, you may be surprised to find that you're passed over for a job based on age, race or gender. Japan does not have anti-discrimination laws and many ads will specifically ask for "female under 25" for office jobs. If you go to one of the job fairs hosted by Dai Job, you'll see booth banners reading "Over 35 OK" (over 50 still seems to be a problem, though). Face it, the Japanese corporate world wants young, attractive employees and this especially holds true when it comes to hiring foreigners.
And the government wants an educated work force, so you're not going to get a working visa if you don't have at least a university bachelor's degree (as required by law) (assuming that you're coming from a country that doesn't have working holiday visas).
If you find yourself being discriminated against (being older than 40; being female for a high-tech job; not being Caucasian) there's no action you can take against the company. Just move on and keep looking, remembering that if the company is going to discriminate against you at the hiring phase, they're probably going to keep treating you the same way after you get the job. And is that the kind of job you want?
But, there is hope. Japan is an aging society and there's a growing need for foreign workers to fill the positions that open up due to retirement or old age, especially in the health care fields. Japan just brought in a lot of trained health care workers this Summer from Malaysia. This trend is expected to grow over the next few years. (The Malaysian workers don't speak much Japanese right now, which is a point of contention in the media. Being fluent in Japanese might give you a significant edge in overcoming any other factor that you might otherwise be discriminated about.)