Building Permits

Your local commune - urbanise department.

However - I would first of all speak to your notaire, the one who handled the purchase of the house. Hopefully in the "acte de vente" you signed they checked to be sure that there is a clause saying the the seller confirms that the house is legal, and that any planning permissions necessary have been done. That will help you, as now you're going to sue them for the costs of applying for retrospective planning permission. If you don't have that clause in the acte, then sorry, but it's all your problem.

Your other option is to just keep quiet, and when you eventually come to sell your house, hope the purchaser doesn't notice that you have conveniently left out the clause saying you confirm the house has planning permission.

Personally, I would handle this situation extremely carefully - I know of a similar situation, where the commune agreed to retrospectively grant planning permission for an extension, but still forced the owner to knock it down and rebuild it as what was built did not comply with insulation / safety / building regulations.

Yes, definitely start with your notaire whose advice should come for free.

Interestingly, we bought our house at much the same time and our notaire insisted that we went to the urbanism person at our commune so as to be able to check that the house as built (c1992) corresponded in all material aspects with the permission that had been granted (which it did) - and that was before we signed the compromise de vente. In fact, even we made the original offer, the notaire insisted that there we incorporated a clause relating to conformité urbanisme. His stance on the matter suggested to me that this was another Belgian case of caveat emptor, that is that it was the buyer's responsibility to check the conformity.

Typically, you will need an architect to file a 'régularisation urbanistique' on your behalf.
I saw this once before- in fact as the new owner you may possibly even be able to get the money for the repairs and permit from the owner- as part of an agreement. Please check with Alex, at www.alexandrupatrichi.eu for more info, he's doing this kind of work and taking the headache out for lots of buyers in the same situation as you! (It's more common than you think!)
Good luck! :-)