Possibilities of contesting Architect's assessment over Stamp Duty?

Hello, we have just received a letter form the inland revenue department,  to say that we must pay a considerable amount more because the real market value of the house we bought is 50 % more than what we really paid for.

When we asked our Notary about the visit of this architect and the first letter of the inland revenue department, she said that it was routine and only to check that the property actually conforms to the official plan submitted. As the plan was correct, we thought there was nothing to worry about.

And just know we receive this.  We really don't understand, as we would have paid happily this if told in the first instance, the architect only asked how many rooms there were, and there was no structural works involved (only repainting, refurbishing, nothing major, and in great part done by ourselves). It seems you are only "charged" for having bought something cheap.

And not only this, we will be charged, as well as the vendor, a "penalty", apparently assuming we have done something illegal by not paying the full stamp duty at the first moment, like ascertaining we did some other exchange of money not in the contract (?).

I find this as the most bizarre and unfair thing that has happened to me in Malta so far.

Somebody here has some experience and knows if we could contest this?