The Taoiseach says the post-Brexit measure was imposed on unionists and nationalists without their consent.
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Irish Prime Minister Leo Varadkar has said he regrets the Protocol being imposed on Northern Ireland without the support of unionists and nationalists.
He told the BBC the measure was working but said he understood why unionists felt it had “weakened the union”.
The Protocol, which keeps Northern Ireland aligned with some EU trade rules, has been a source of tension since it was enacted in 2021.
Unionist parties argue it undermines Northern Ireland’s place within the UK.
Mr Varadkar became Taoiseach, or prime minister of Ireland, for the second time last month.
He previously served in the role between 2017 and 2020, and therefore played a part in the Brexit talks that ultimately led to the creation of the Protocol.
The Protocol is an agreement between the EU and UK which allows goods to be transported across the Irish land border without the need for checks.
Before Brexit, it was easy to transport goods across this border because both sides followed the same EU rules but, after the UK left, special trading arrangements were needed so that this could still happen.
The land border is a sensitive issue because of Northern Ireland’s troubled political history. It was feared that cameras or border posts – as part of these checks – could lead to instability.
The EU has strict food rules and requires border checks when certain goods – such as milk and eggs – arrive from non-EU countries.
Asked by the BBC’s economics editor Faisal Islam whether anything could have been done differently during the Protocol talks, Mr Varadkar said his main regret was that the measure had been “imposed on Northern Ireland without the support of both communities”.
“In the same way Brexit was imposed on Northern Ireland without the support of both communities, the Protocol was imposed on Northern Ireland without the support of two communities,” he said, laying some blame on the fact Northern Ireland’s government “was not functioning”.
But Mr Varadkar said the Protocol was working economically and that the absence of a hard border between Northern Ireland and the Republic was proof of this.
Speaking at the World Economic Forum in Davos, he also said Northern Ireland’s economy was “outperforming the UK economy”.
But Mr Varadkar said he could understand why unionists and unionist politicians felt the Protocol had “lessened the links [and] weakened the union between Northern Ireland and Britain” without them “having a proper say as to how it operates”.
Mr Varadkar’s interview, his first with a British outlet since returning to office, came amid an ongoing stalemate at Stormont, the Northern Ireland parliament.
There has been no functioning devolved government at Stormont since February 2022 after the Democratic Unionist Party (DUP) withdrew from the institution in protest against the Protocol.
The party has continued its boycott at Stormont and is demanding fundamental change to the Protocol before it considers a return to the assembly.
Mr Varadkar said he hoped a fresh agreement between the EU and UK could be reached “sooner rather than later”, describing UK Prime Minister Rishi Sunak as someone he believed would “go about doing business and getting things done”.
“The possibility of an agreement… in the next couple of months is very real and, with reasonableness and flexibility on both sides, it can be achieved,” he added.