Micheal Martin has called for a reset of the relationship between the UK and the EU to resolve issues stemming from the Irish Sea border.
The Taoiseach lamented the deterioration of diplomatic relations between the bloc and the UK following rows over Brexit and the supply of Covid-19 vaccines.
The Northern Ireland Protocol, designed to avoid a hard border in Ireland, has caused unrest among both unionists and loyalists.
In an interview with the Financial Times, Mr Martin said he had told the EU the bloc's relationship must be "constructive".
He said: "I think we need to reset the relationship.
"I've made it very clear to our European Union partners that the British-Irish relationship is a unique one, historically rooted.
"We're both joint custodians of the (Good Friday) Agreement and nothing can come between us in respect of making sure that we work constructively together.
"That's our aim and our objective as a Government - to maintain a constructive relationship with Britain."
The Taoiseach said he had argued "the only future has to be a constructive UK-EU relationship".
The relationship, already damaged by Brexit, deteriorated further due to the EU's brief suspension of the protocol in a row over vaccines.
The UK also suspended elements of the protocol unilaterally by suspending customs checks on goods travelling between Britain and Northern Ireland, a move dubbed "silly" by Mr Martin.
The premier said the EU had already done a lot to "facilitate the uniqueness" of the protocol, but acknowledged there was "work to be done... to see what we can fine-tune".
He called for the use of special committees to tackle difficulties arising from the protocol, which have been provided for under the Withdrawal Agreement.
He said: "We've got to try to work those committees to see can we deal with those issues and make life as easy as possible for businesses."
Despite these setbacks, Mr Martin believes the relationship can get back on track.
"I think it makes sense for Britain that it really works on its relationship with the EU. The EU is ready to engage," he said.
He told the paper UK officials had been more constructive in recent weeks.
The move towards a "win-win" deal on the supply of Covid-19 vaccines across Europe and the UK was a "very important" sign, he added.