The India side
In India the rent is income from house property, taxed after a flat 30% standard deduction under Section 24, which you get whatever you actually spent, and after home-loan interest, at slab rates. As a non-resident landlord, your tenant must deduct TDS under Section 195 on the gross rent, from the first rupee with no threshold, which over-deducts against your real Indian tax. You recover the excess by filing an Indian return, or reduce it up front with a lower-deduction certificate. India taxes the rent whatever Japan does.
Japan: which resident are you
Japan does not tax all residents alike, and this is the key to your Indian rent. If you are a non-permanent resident, meaning you are not a Japanese national and have been resident in Japan for five years or less within the last ten, Japan taxes your foreign-source income, and Indian rent is foreign-source, only to the extent you pay it into or remit it to Japan. So rent that stays in your Indian account is outside Japanese tax during those years.
There is a catch in how remittances are read. If you send money to Japan in a year, the tax office treats the remittance as coming from your foreign income first, up to the amount remitted, so even a general transfer of savings can drag the rent into the Japanese net. Once you become a permanent resident, over five years, Japan taxes the rent on its worldwide basis whatever you do with it, computing its own net figure and giving a credit for the India tax. So the same rent is outside Japanese tax for a non-permanent resident who leaves it in India, and taxed with a credit once you cross into permanent residence.