Two different fronts: the cost side and the sale side
A property valuation gets questioned in one of two ways, and they are governed by different sections, so it helps to know which one the notice is about. The cost side is what you say the property cost you, the original price, the 1 April 2001 fair-market value, or the improvements. If that looks too high, the gain looks too low, and the officer challenges it to raise the gain.
The sale side is what you say you sold it for. If the declared price is below the stamp-duty value the state uses to charge registration duty, the law suspects under-declaration and can tax you on the higher stamp value instead. Each front has its own rule and its own defence, and a single notice sometimes raises both, so the first step is simply to identify which value is under attack.
The cost side: Section 55A and the Valuation Officer
When the officer thinks your cost or 2001 value is inflated, the route is a reference to a Departmental Valuation Officer under Section 55A. The Valuation Officer independently assesses the fair-market value, and the assessment is made on that figure. This is exactly why the original claim should rest on a registered valuer's report tied to the circle rates, comparable sales of the period and the property's real attributes, rather than an optimistic round number.
A well-supported report does two things. It makes the initial claim credible, so a reference is less likely, and if a reference does happen, it gives you a professional valuation to set against the Departmental Valuation Officer's, which frequently narrows or closes the gap. An NRI does not need to attend in person; a practising CA handles the correspondence, the submissions and the valuer coordination from the Indian side.
The sale side: Section 50C and the stamp-duty value
On the sale side, Section 50C says that if you sell land or a building for less than its stamp-duty value, the stamp-duty value is treated as your sale consideration for computing the gain, even though you received less. The law allows a tolerance band of up to 10%, so where the stamp value does not exceed 110% of your actual price the shortfall is ignored and the real price stands, but a larger gap pulls the higher stamp value into the computation.
There is a genuine defence where the stamp-duty value itself is too high, which happens when the circle rate has not kept pace with a depressed local market or the property has a defect the circle rate ignores. In that case you can ask the officer to refer the fair value to the Valuation Officer, and if the Valuation Officer's figure is lower than the stamp value, that lower figure is used. So an unfair stamp value is contestable rather than final, provided you raise it correctly and on time.