Salaries are all over the place. The lowest salaries for developers are about ¥3 million per year, and on the high end, I know of developers making ¥25 million plus per year.
Historically, Japan hasn’t seen software development as a skilled profession. Companies would hire university students based primarily on their university name (not degree), and assign a certain percentage of them to be developers. After hiring the new grads, they’d spend about three months educating them on how to program.
As you can imagine, this meant the average skill level of developers in such companies was pretty low, as the majority had no interest or aptitude for it. Wages reflected this, and developers were paid the standard salaryman wage (your age * ¥10,000 per month).
Since then, things have started to change. Some companies have awakened to the fact that not all developers are interchangeable, and having skilled professionals can make a big difference. With this comes a rise in salaries.
You’ll probably find the highest salaries at companies that both value developers and are highly profitable. That’s why companies like Google and Facebook pay well, as do things in the financial sector.
For talented developers, based off anecdotal evidence, decent but not exceptional salaries are ¥5 million for just getting started, ¥7 million for several years experience, and ¥9 million up for someone more experienced.