Taxes on foreign income

I have been living in Japan for 5 years. I pay tax in Japan on my Japanese income. I have been paying tax in Australia on Australian income at the non-resident rate, but now I have been told I have to submit a tax declaration in Japan on the Australian income. Wouldn't that mean I would be taxed twice? Are there any english speaking tax specialists to help foreigners with their tax questions? Thanks.

After 5 years of living in Japan, you will be classified as a "permanent resident" in terms of Japanese income tax as explained here:
http://www.japan-guide.com/e/e2206.html

It means you will have to pay taxes on all income from inside and outside of Japan.

However, thanks to a tax treaty between Australia and Japan, you should be able to avoid doubel taxing. I recommend to consult a tax professional for advice. Or search the internet for "japan australia tax treaty" or similar. The local tax office should also be able to help (in case you speak Japanese).