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If you live in japan, you should file a japanese tax report. Wheter you should file a US tax report really depends on tax treaties between japan and US, which I don't know much about.

But in general, if your country of residence (in your case, japan) has a tax treaty with the other country (in this case, the US), you don't file a tax report, you only claim the taxes paid to the foreign country as a deduction in your country. For example, as a canadian living in canada, if I pay US taxes due to dividends on a US stock, I can claim that amount on my canadian tax report and be done with it.

If you country doesn't have a tax treaty in place, you can either file a tax report or not, whichever is most convenient to you. For example, as a canadian living in canada, I paid 10$ in taxes to France because of dividends on Total SA in my RRSP account. I cannot claim that tax on my canadian tax report because it's in a tax-protected account, but I sure as heck ain't filing a french tax form for 10$. If it was 10k$, then I'd probably file one.

So the answer really is in the Japanese tax code. If you can claim a deduction on foreign taxes, then you don't file a foreign one. If you can't, then it's up to you.

One more thing: you never have to file a foreign tax report (with one exception: US citizens have to file a report even if they don't live in US). I would strongly suggest that you file a canadian tax report IF you intend on coming back to live in canada, but other than that, you should file only reports from:
1-The country (and/or jurisdiction, province, state, city) you live in;
2-If you believe you've paid more than your share and will get a meaningful reimbursment.

One last thing: filing a US tax report is not the hell that americans make it appear to be. A simplified 1040NR (the tax form for Non-Resident) is 2 pages long, one of them being your infos and dependants. Last time I filled one, filling my adress was the most challenging thing on that form.
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