The five-year line that changes everything
Japan sorts residents into two tiers for foreign income. If you are not a Japanese national and you have lived in Japan for five years or less within the last ten, you are a non-permanent resident. Japan then taxes your Japanese income in full, but your foreign income, including a gain on Indian mutual funds, only to the extent you pay it in or remit it to Japan.
Once you have been in Japan for more than five of the last ten years, you become a permanent resident for tax. From that point Japan taxes your worldwide income, so an Indian mutual fund gain is taxable in Japan whether or not you bring the money in. Japan's top personal rate, national plus local plus the surtax, reaches about 55%, though some fund gains are taxed instead at a lower flat rate of around 20%, depending on the fund. Either way, the cheap time to realise Indian gains is while you are still a non-permanent resident.
The same-year remittance trap
Japan does not trace your money. Under its remittance rule, any amount you bring into Japan in a year is treated as carrying that year's foreign income first, up to the amount you remit. So if you sell an Indian mutual fund and, in the same year, send yourself money into Japan for any reason, that remittance can be matched against the gain and taxed, even though the actual sale proceeds never left India.
The practical lesson is to separate the two. If you realise an Indian gain as a non-permanent resident, avoid remitting money into Japan in that same year, or keep any remittance to funds that are clearly not that year's foreign income. A year with a sale and no inward remittance keeps the gain out of Japanese tax.
The India side, and where the treaty helps
On the Indian side, when you redeem Indian mutual funds the fund house deducts TDS under Section 195 (Section 393 from FY 2026-27). Where the gain is taxable in India, the India-Japan treaty lets Japan give you a credit for the Indian tax you paid, so the same gain is not taxed twice. You claim the Indian position with a Tax Residency Certificate and Form 10F (Form 41 from FY 2026-27).
One income type has no relief. NRE interest is exempt in India, so when Japan taxes it, as a permanent resident or on remittance, there is no Indian tax to credit and it is taxed in Japan in full. That is worth remembering when you plan which Indian income to bring into Japan and when.
A worked example
Arjun has lived in Tokyo for four years and is a non-permanent resident. He holds Indian mutual funds sitting on a large gain and plans to move back to India eventually.
He sells the funds this year and leaves the proceeds in his Indian account, and he makes sure not to remit any money into Japan during the same year. The gain is foreign income he did not bring in, so Japan does not tax it, and on the Indian side he handles the TDS and any treaty credit. Had he waited until his sixth year, he would be a permanent resident and Japan would tax the gain on his worldwide income whatever he did with the money. Selling inside the window, and not remitting that year, kept the gain out of Japanese tax.