What you actually own, and when the clock started
In a cooperative housing society, you do not hold the flat by a conventional title deed; you hold shares in the society, and those shares carry the right to occupy your flat. When you sell, you transfer the shares and the occupancy rights together, and that bundle is a capital asset under Section 2(14), so the gain is computed the ordinary way under Section 45, with your cost and the sale price.
The valuable point is when your holding period began. For a society flat it runs from the date the society allotted the flat to you, or issued the share certificate, not from any later registration or the day you took possession. The tax department itself accepts this: CBDT Circular 672 extended to cooperative societies the earlier position that an allotment is the date of acquisition. So a flat you were allotted years ago is long-term even if the formal paperwork came later, and under Section 2(42A) long-term means held more than 24 months, which puts the gain at the lower rate rather than being taxed as a short-term gain. Keeping the allotment letter and share certificate is what proves this.
The NRI TDS, and the society formalities
The society structure sometimes confuses the TDS. Because a society flat is technically shares, buyers occasionally think of it as a share purchase and overlook the property-sale withholding. For an NRI seller that does not change anything: the buyer must deduct TDS under Section 195, on the sum chargeable, whenever they pay a non-resident. The 1% rate that applies to a resident seller of property never applies to an NRI in any case, so whether the flat is called shares or immovable property makes no difference, Section 195 governs, and a lower-deduction certificate brings the withholding down to your real gain.
Separately, the society will have its own requirements for the transfer: a no-objection certificate, a transfer fee or premium, and recording the new member in the share register. Those are governance matters and are entirely separate from the tax, they do not change the capital gain or the TDS, though the sale cannot complete without them. A practising CA fixes the holding period from the allotment date, computes the gain correctly, and sets up the Section 195 position with a lower-deduction certificate, while the society formalities run in parallel.