The EU has introduced controls to prevent the export of COVID-19 vaccines from the bloc to Northern Ireland.
Brussels triggered Article 16 of the Northern Ireland Protocol that forms part of the Brexit withdrawal deal.
The move comes amid a row with vaccine maker AstraZeneca over the supply of vaccine doses to the 27 members of the bloc.
The EU decision to activate Article 16 will frustrate any effort to use Northern Ireland as a back door to bring vaccines into the rest of the UK.
Under the terms of the protocol, goods should be able to move freely between the EU and Northern Ireland as the region remains in the single market for goods and still operates under EU customs rules.
Stormont's First Minister Arlene Foster has called the latest move by Brussels an "incredible act of hostility".
She said: "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."
The regulation means Northern Ireland will be considered an export territory for the purposes of vaccine sent from the EU/the Republic of Ireland.
Northern Ireland's vaccines arrive from the rest of the UK at present so those will be unaffected.
The DUP leader added: "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."
Mrs Foster spoke to Prime Minister Boris Johnson and Cabinet Office minister Michael Gove about the issue on Friday evening, and called for a "robust response" from the UK government.
A Number 10 spokesperson said Mr Gove had talked to European Commission Vice President Maros Sefcovic to express the UK's concern over a lack of notification from the EU about its actions in relation to the Northern Ireland Protocol.
The spokesperson said the UK would now be carefully considering next steps.
The European Commission 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."
Ireland's premier Micheal Martin is in discussions with European Commission President Ursula Von Der Leyen to express his concerns, according to an Irish government spokesperson.
Louise Haigh MP, Labour's Shadow Northern Ireland Secretary, said the EU's move was "deeply destabilising and undermines the huge efforts being made to make the Protocol work".
"Unilateral actions like this do nothing to aid the stability in Northern Ireland which the Protocol was designed to preserve."
Analysis: The 'nuclear option'
By David Blevins, Ireland correspondent
Some have described Article 16 as the "nuclear option".
It effectively allows either the EU or the UK to override the Northern Ireland part of the Brexit deal.
The Northern Ireland Protocol was negotiated to avoid a border on the island of Ireland.
Instead, they created a border in the Irish Sea - between GB and Northern Ireland - much to the angst of Unionists.
That meant Northern Ireland was the only part of the UK still able to trade freely with the EU.
By invoking Article 16, the EU has arguably created the need for a land border on the island after all.
Unionist politicians say the EU has now left the UK government with little option but to invoke it too.
Twenty-nine days after the end of the transition period, the Northern Ireland deal hangs by a thread.