Speaking on Sunday, foreign minister Simon Coveney said that any move to trigger Article 16 and suspend the protocol would have “serious” consequences.
Mr Coveney said continuation of the free trade agreement between the UK and EU was “contingent on” the Northern Ireland deal continuing to operate.
Suspending the free trade agreement would see British businesses hit with new tariffs and even worse terms than they enjoy now outside the single market.
“I believe that if the British government essentially refuses to implement the protocol, even with the extraordinary flexibilities that are now on offer, and instead looks to set it aside then I think the EU will respond in a very serious way to that,” Mr Coveney told broadcaster RTE.
The minister added: “It means that the Trade and Cooperation Agreement that was agreed between the British government and the EU was contingent on the implementation of the Withdrawal Agreement, which includes the protocol.
“One is contingent on the other. So if one is being set aside, there is a danger that the other will also be set aside by the EU.”
The Irish foreign minister said the consequences would not include a hard border between Ireland and Northern Ireland, which he said the EU would not reintroduce.
Ireland is not the only country to issue the warning. Belgium’s deputy prime minister Vincent Van Peteghem made similar comments regarding the free trade agreement in an interview with Bloomberg TV on Friday.
Speaking to the same broadcaster Mr Coveney said triggering the protocol would be “a significant act that would damage relationships between Britain and Ireland”.
Giving his assessment of the situation, he added: “I think all the evidence now suggests that the British government are laying the foundations to trigger Article 16.”
The interventions come after Lord Frost, the UK’s Brexit negotiator, said the drastic course of action was “very much on the table and has been since July”.
The protocol was designed to stop a hard border from appearing between Northern Ireland and the Republic, but also puts controls on trade between Britain and the EU.
The UK has taken issue with the controls it signed up to and says it wants the agreement to be changed. The EU has presented proposals, but the UK says they do not go far enough.
Some speculative reports suggest Mr Johnson wants to trigger Article 16 – the agreed mechanism to suspend it – after the Cop26 climate summit is over and Britain is no longer in the spotlight.
On Saturday former Tory MP John Major said it would be “colossally stupid” to trigger Article 16, branding the approach “absurd”.
And on Sunday Labour leader Keir Starmer suggested that Boris Johnson was “constantly trying to pick a fight on things like this so he hopes people don't look elsewhere” – such as sleaze scandals.
Sir Keir would not be explicitly drawn on whether his party would oppose the government in triggering Article 16 – a mechanism built into the Northern Ireland protocol that effectively suspends the deal. There is not expected to be a vote in parliament on the matter.
But he said: “I don't think that triggering Article 16 will resolve the dispute in relation to the Protocol in Northern Ireland. That isn’t in the interests of the communities in Northern Ireland or businesses in Northern Ireland. What is in their interests is resolving the issues.
“Because of the way the Protocol was drafted, because of what the prime minister signed, it is perfectly true that there are checks from Great Britain to Northern Ireland – we want to reduce those.”
The Labour leader added: “What I am saying is don’t rip up the protocol because that has that very important central purpose, which is to protect the no border in Northern Ireland.”
Sir Keir said that as an alternative he would like to see “both sides sitting down and resolving this”. More talks between Lord Frost and his EU counterpart Maros Sefcovic are scheduled for next week.
The Labour leader, who was previously seen as a major supporter of a second referendum, said repeatedly throughout the interview that he wanted to “make Brexit work” – a slogan he used in his recent party conference speech.
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