The Taoiseach Micheál Martin is 'in talks' with European Commission President Ursula von der Leyen over the tightening of rules on exports of coronavirus vaccines.
Brussels triggered Article 16 of the Northern Ireland Protocol that forms part of the Brexit withdrawal agreement.
The move comes amid an ongoing row with vaccine maker AstraZeneca over the supply of vaccine doses to the European Union.
Under the terms of the protocol, goods should be able to move freely between the EU and Northern Ireland - but triggering Article 16 temporarily places export controls on the movement of vaccines.
It means Northern Ireland will be considered an export territory for the purposes of vaccines sent from the EU.
A Government spokesman said: "We are aware of the issue and the Taoiseach is currently in discussions with European Commission President Ursula von der Leyen to express our concerns."
The European Commission said it is not a ban, and that it just wants to know how many supplies are leaving the bloc and where they are going.
It said: "Exports of goods from Northern Ireland to other parts of the United Kingdom cannot be restricted by union law unless this is strictly required by international obligations of the union.
"Therefore, movements of goods covered by this regulation between the union and Northern Ireland should be treated as exports."
It added: "This is justified as a safeguard measure pursuant to Article 16... in order to avert serious societal difficulties due to a lack of supply threatening to disturb the orderly implementation of the vaccination campaigns in the member states."
Earlier, Northern Ireland First Minister Arlene Foster branded the move 'aggressive and shameful'.
In a statement, she said: "This is an incredible act of hostility.
"By triggering Article 16 in this manner, the European Union has once again shown it is prepared to use Northern Ireland when it suits their interests but in the most despicable manner - over the provision of a vaccine which is designed to save lives.
"At the first opportunity the EU has placed a hard border between Northern Ireland and the Republic of Ireland over the supply chain of the coronavirus vaccine.
"With the European Union using Article 16 in such an aggressive and most shameful way, it is now time for our government to step up.
"I will be urging the [British] prime minister to act and use robust measures including Article 16 to advance the interests of Northern Ireland and the rest of the United Kingdom."
The European Medicines Agency (EMA) earlier approved the AstraZeneca vaccine for use across the bloc.
Additional reporting: IRN