@sammylove
- Is your accountant thoroughly familiar with the tax treaty? rules on residency are right in it: https://www.mofa.go.jp/region/asia-paci/australia/agree0801.pdf
- I'm neither a lawyer nor your lawyer, but I'd wager quite a bit that you're a resident of Japan for tax purposes (https://www.oecd.org/tax/automatic-...istance/tax-residency/Japan-Tax-Residency.pdf).
- since you were doing the work while in Japan, you owe Japan income taxes.
- You should not owe income taxes to Australia because you owe them to Japan, but if there's something wonky where you pay both taxes, you should get a tax credit making it so that you only end up paying basically the higher of the two tax obligations (with the caveat that they may not recognize all of the deductions that the other grants).