This row stems from two of the biggest stories in Europe over the past few years: Brexit and the pandemic.
"I think that the mask slipped on Friday night because the European Union and others had been lecturing everybody ... that there could never be under any circumstances whatsoever any kind of hard border on the island of Ireland, and that to do anything to over-ride any of the Protocol provisions would be an anathema, and then in one fell swoop on Friday night it did both of those things ... never mind the fact that it was aimed at vaccines, which is aimed at helping people overcome this bad Covid pandemic", he told the BBC's Sunday Politics programme.
The commission has since made clear the new measure will not trigger controls on vaccines shipments produced in the 27-nation bloc to the small territory that is part of the United Kingdom bordering European Union member Ireland.
THE EU has been accused of taking a play straight out of the Donald Trump book on diplomacy after attempting to block vaccine supplies to Northern Ireland. But now it's the EU's vaccine row that's sparked fears of checks on the border.
However Mr Martin laid some blame at the door of AstraZeneca, saying there is a "strong sense across Europe" that the Anglo-Sewdish jab manufacturer has not delivered on commitments around the vaccination.
But isn't this about vaccines?
It came as Berlin and Rome issued similar threats to vaccine providers.
"In my view, it would be a hugely retrograde step for Northern Ireland if the protocol was undermined in any way and that's why we moved so quickly last evening to ensure no damage was done". That automatically means there must be a hard border, so the EU's Single Market can be protected from flooding by foreign goods.
"There's clearly panic at the highest levels of the Commission, and the issue of the Northern Ireland agreement has been swept up in this bigger issue of the EU's poor vaccine performance", he said.
If you didn't think it was already incredibly complicated, well, hold on to your hats.
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Investigators have made a priority of exploring whether the attack was planned in advance by groups like the Proud Boys. They held rallies supporting President Donald Trump in the Pacific Northwest earlier this year.
The vaccine, developed by AstraZeneca and the University of Oxford, is the third approved by the EMA, developed by Pfizer / BioNtech on 21 December and Moderna on 6 January. It's thought around 60 percent of the agreed vaccine will be delivered to the EU.
The European Commission also revealed it was setting up controls on vaccine supplies from the EU to outside the bloc, while insisting it was not a ban. The most acute shortage - that we are now aware of is in Germany.
She said this represented a 30% increase on the previous amount.
The export controls come as Brussels locks horns with AstraZeneca over the delayed delivery of tens of millions of doses of its COVID-19 vaccine. The report is expected in the coming days.
The Taoiseach then contacted President von der Leyen and "articulated the very serious implications the move would have" on the protocol itself.
Mr Martin said the move to trigger Article 16 initially was "certainly not" an act of hostility by the European Commission.
Northern Ireland's First Minister Arlene Foster described the move by the European Union as an "act of hostility" and has urged Johnson to replace the "unworkable" protocol.
"The Commission is not triggering the safeguard clause", it said in its statement, adding that the restricting regulations have yet to be finalised and were not due to be adopted before yesterday.
Mr Martin said the construction sector would reopen once Covid-19 cases drop below 1,000 each day.
Clement Beaune, the French Europe minister, threatened sanctions against the Anglo-Swedish company if it emerged that Britain had been given priority, saying on Sunday: "If there is a problem and other countries have been favoured - for example the United Kingdom over us - then we will defend our interests".