GST is on supply of goods or services or both. If flat is under construction then GST will be charged at 12% on remaining payment.
However government has come up with a warning for builders that they should not charge extra to customers and pass down the benefits of input credit which was not earlier available.
You need to discuss with your builder, whether EMI will increase or decrease due to availability of input credit.
If flats are fully constructed than I doubt there be any input remaining and in that case EMI cost will go up.
However if construction percentage is below 25%, cost may come down due to availability of input on Cement, and other materials.