Tanaiste Leo Varadkar has warned Boris Johnson the UK will not get a better deal if it triggers Article 16.
The UK's Brexit Minister, Lord Frost, said on Wednesday it is not "inevitable" that the Government would take that action, but said it would be "our only option" if negotiations with the EU fail.
Such a move is likely to spark retaliation from the EU, with talk of a suspension of the EU-UK trade deal that could result in a trade war.
Leo Varadkar said suspending the protocol would be a "big mistake" and urged the Prime Minister not to do so.
"We have an agreement in relation to Northern Ireland, we have an agreement in relation to trade with the European Union.
"Don't jeopardise that agreement," he said.
"You were part of negotiating us, you own it, it was hard-won.
"It's a mistake to think that, by escalating tensions, by withdrawing from any part of it or trying to withdraw from any part of it, that you'll end up with a better deal.
"You won't."
Mr Varadkar said a suspension of the EU-UK trade deal would require a year's notice, which would spark further uncertainty for businesses in Northern Ireland, the Republic and the UK.
He said: "I think that would be a big mistake.
"The uncertainty that was created by Brexit went on for years.
"I think it would be a big mistake for the British Government now to reopen that uncertainty.
"I'd hate us to be talking again about a no-deal Brexit or a cliff edge, or any of those terms that we'd forgotten and almost stopped using.
"Any attempt to trigger Article 16, I think, would be bad news for business in Northern Ireland, here in Ireland and indeed in Britain."
The Irish Government has begun reactivating no-deal contingency planning in preparation for a potential unravelling of the Brexit deal.
Talks between London and Brussels over the contentious protocol remain deadlocked and there is growing speculation that the UK is poised to trigger Article 16 in the coming weeks.
