The Commission has sent a formal notice to Denmark over the issue, reports Altinget.
According to the purchase agreements, suppliers of the new military equipment must place orders in Denmark in return for doing business with the military, in order to ensure some of the value of the investments remains in Denmark.
But an EU directive on public purchases of military hardware states that member states must not enter into such agreements unless for reasons of national security.
Denmark has previously tried to convince the EU Commission that the purchase agreements do not break EU rules, according to Altinget's report. The formal notice from the EU represents a rejection of the Danish claim.
But Denmark is expected to stick to its guns over the matter, the media reports, with compensation payments likely to be demanded should the Scandinavian country accept the EU complaint or lose a trial over the matter at the European Court of Justice (ECJ).
The Danish Business Authority (Erhvervsstyrelsen) has confirmed receiving the written notice, which is the first formal step towards an ECJ trial, but declined to comment further to Altinget.
EU member states are given the option of responding to such formal notices before the EU Commission makes a final assessment on whether tractates have been broken. The Commission can then decide to bring the issue before the ECJ.
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