I answered a related question () earlier. The answer contains some anecdoctal horror stories of people with monthly salaries to the tune of $1,500 and some other (more solid) data.
I can think of these reasons as to why the salaries are so low (there are exceptions):
Japan is the one of the world’s leading video game nations, with many college graduates, for example, dreaming of working for companies in that sector. In other words, some companies take advantage of them having a somewhat cool image.
Generally speaking, programmers in any kind of company in Japan get relatively low salaries. PHP programmers and C experts, for example, can expect an average salary of $54-$68,000 per year (reference: http://www.slideshare.net/yandod…).
Needless to say, there are exceptions, depending on the company, the level of experience of the programmer in question etc.
The Japanese video game market is shrinking rapidly. According to video game magazine publisher Enterbrain, the local market for video game soft- and hardware shrank 6.9% year-on-year to $6.4 billion in 2009 (it already contracted in 2008).