Hi
There are two approaches here:
1. Considering the amount received as a capital receipt and reducing it from your cost of acquisition of the flat.
2. Considering the amount received as a revenue receipt and paying taxes accordingly as Other Sources income.
Although Approach 1 will reduce your Cost of acquisition and thereby increase your capital gains if you sell this property later in future, following this approach is advisable. If you wish to follow approach 1, make sure you get a statement from the builder clearly stating such payments made by him to you and arriving at the final cost of acquisition to you.