You have to pay acquisition VAT.
The VAT rules (but not the rates) are standardised across the EU. Here is the UK example from VAT notice 725
3. Supplies to customers registered for VAT in another Member State
3.1 How is VAT accounted for?
The normal VAT treatment of goods supplied between VAT-registered traders in different Member States is as follows:
- the supply in the Member State of dispatch is zero-rated (how this applies in the UK is explained in more detail in section 4), and
- VAT is due on the acquisition of the goods in the Member State of arrival and is accounted for by the customer on their VAT Return at the rate in force in that Member State (how this applies in the UK is explained in more detail in section 7)
Section 7 is worth reading.
Here is what the EU say
What is an intra-EU supply?
An intra-EU supply of goods is a transaction in which goods are dispatched or transported by (or on behalf of) the supplier or the customer from one EU country to a destination in another EU country.
Supplier in EU country 1 Customer in EU country 2
Business (taxable person) Business or
Non-taxable legal entity
(such as public body) acting as such
the transaction is exempt (Article 138(1) VAT Directive), although there are some exceptions
When an intra-EU supply takes place, the customer makes a corresponding intra‑EU acquisition. This is a transaction that is normally taxed.
The right to deduct
Although an intra-EU supply in these circumstances is normally exempt, the input VAT incurred on goods and services used for the purposes of making that supply may be deducted by the supplier (Article 169(b) VAT Directive). This is because the corresponding acquisition is taxed.
An Irish electronics manufacturer supplies circuit boards to a French company for use in the French company’s factory in Montpellier.
The Irish company’s supply is exempt from Irish VAT as an intra-EU supply. However, the input VAT the Irish company incurs is deductible.
The French company makes an intra-EU acquisition of goods, which is subject to French VAT.
Where you pay VAT and how much you pay depends on whether you (or your company) are VAT registered.
Whether you (or your company) have to be VAT registered depends on your (its) annual turnover (this is the law where I live, this may differ in other EU countries).
You must tell HM Revenue and Customs (HMRC) about goods that you bring into the UK, and pay any VAT and duty that is due.
As a VAT-registered company you can reclaim VAT paid out (that's the way VAT works) but you have to charge VAT on goods produced using the equipment you purchase and when you sell that equipment.
It's probably irrelevant, but by d.o.o. I guess you mean the type of limited liability company formed in countries like Slovenia.