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Mr Martin said it should not be assumed that the British will trigger Article 16 amid heavy speculation that the UK Government is preparing to suspend the agreement.
The Taoiseach called for extensive engagement on both sides to avoid the situation coming to pass.
What's important now is that we double down on dialogue and engagement
He told the Dail: “Discussions are still ongoing. I would just sound a note of caution that we don’t automatically assume that anything is going to be triggered.
“I think that’s important. We don’t want a kind of a self-fulfilling prophecy either.
“My views are very strong and I don’t think there’s a need to trigger Article 16. I believe it would be wrong to do so.
“What’s important now is that we double down on dialogue and engagement.
“That is happening, ministerial engagements with our counterparts are happening.
“The opportunities will be taken in the context of those engagements to raise these issues and to point out the primacy of continuing dialogue between the European Union and the United Kingdom.”
Speculation is rife that the UK is preparing to trigger the clause in the Brexit deal – which would effectively suspend elements of the arrangements – which have prevented a hard border on the island of Ireland, but stoked tensions in unionist communities in Northern Ireland.
Mr Martin warned that the move would impact Northern Ireland’s dual access to European and UK markets provided under the protocol.
He said: “Trade would be disrupted, ultimately. Access to the single market is important to people in Northern Ireland and to businesses in Northern Ireland.
“It’s having a beneficial impact. Any triggering of Article 16 could ultimately jeopardise, in the shorter term, that access.
“What’s important now is that we double down on dialogue and engagement.”
One would have formed the view that was maybe an effort to almost torpedo the Sefcovic package before it was published
Mr Martin said the European Commission vice president Maros Sefcovic had put forward a robust set of proposals to tackle operational issues around the protocol.
But he said a demand by UK Brexit Minister Lord Frost that the oversight role of the European Court of Justice (ECJ) on the operation of the protocol be dropped, in advance of those proposals being made, was an attempt to “torpedo” the package.
“I think it’s very regrettable that in advance of the publication of the Sefcovic package, that Lord Frost announced the issue around the ECJ,” he said.
“One would have formed the view that was maybe an effort to almost torpedo the Sefcovic package before it was published.
“But I don’t think it had an impact, in any event.
“I think the Sefcovic package is strong, it’s substantive, it deals with SPS, customs and deals with the supply of medicines, which were all of the issues that people had raised.
“There were legitimate issues that people had raised in relation to the operation of the protocol on all sides.”
Mr Martin spoke about the issue with DUP leader Sir Jeffrey Donaldson on Wednesday.
Afterwards, Mr Donaldson called on the Taoiseach to use his influence in Brussels to find a solution that works for unionists.
He said: “We had a useful discussion. Dublin is a key influencer in Brussels.
“They must use that influence to reach a sensible outcome which is sustainable and can command the support of unionists in Northern Ireland.
“Brussels’ devotion and loyalty to the protocol should not overshadow the wider interests of peace and stability here.”