I am not a solicitor but a qualified tax consultant
It is 25% of total cost so it would be 25% X (site cost plus Buliding cost less VAT)
Here is an example from tax manual published by the
New houses and apartments
Owner occupiers (including first-time buyers)
In general, the rates of stamp duty are now the same for new and second-hand residential property. However, owner occupiers who buy new houses or apartments may qualify for further reliefs:
If the new house/apartment is not larger than 125 square metres/1345 square feet, and qualifies for a floor area compliance certificate (issued by the Minister for Environment, Heritage and Local Government), it is exempt from stamp duty, provided the purchaser is an owner occupier (s. 91A, SDCA 99).
If the house/apartment is larger, and the purchaser is an owner occupier, duty is payable on the higher of:
The site cost
25% of the total cost of the house.
The duty is payable at the rate appropriate to the amount on which duty is charged, rather than at the rate appropriate to the total price (s.92, SDCA).
Example
An owner occupier (who is not a first time buyer) buys a new house for €800,000. The site element is €150,000. The house is too large to qualify for exemption under s.91. However, it qualifies for relief under s.92. Duty is payable on €200,000 @ 4% = €8,000 (i.e. duty is payable on 25% of the cost).
If the site element were €250,000 instead of €150,000, duty would be payable on €250,000. The amount payable by an owner occupier who was not a first-time buyer would be €250,000 @ 4% = €10,000.
To clarify section 92 SDCA 1999 states
...........on an amount which is the greater of-
(a) any consideration paid in respect of the sale of that land, and
(b) 25 per cent of the aggregate of the consideration at paragraph (a) and the consideration paid, or to be paid, in respect of the building of the dwellinghouse or apartment on that land.";