You should really ask the council directly for a proper answer on it.

Under the Housing Act and the relevant accompanying statutory instruments, there is something which is known as the 'Cost Floor'. This means that, for a period of 15 years after the property was built the authority (or housing association) can recover the costs of building the property, acquiring the plot and doing any site development works.

If that value is higher than the sale price (the price you'll pay for the property after discount) but lower than the market value (the value before discount) then your discount will be reduced accordingly. So, assuming the following figures as an easy example:
Market Value = £150,000
Discount = £40,000
Sale Price = £110,000
If the build costs etc (the cost floor) were £125,000 the authority would deduct £15,000 (being the difference between the sale price and the cost floor) from your discount meaning your final discount would be £25,000 and the final sale price would be £125,000.

If the costs exceed the current open market value of the property then you will receive no discount and pay the open market value. So, if the property is worth £100,000 and the costs of building it etc were £125,000 you would pay £100,000 regardless of how much discount you could get.

So, to answer your question, the Council cannot refuse your application just because the house is new (unless it has been specially adapted for disabled use or one of the other exemptions in the Act). But, they can recover their costs in developing and building the house up to the current market value. So you can still exercise your Right to Buy, you just won't necessarily receive much of a discount, if any at all.

@da_rule -- this explanation is perfect, thank you very much.