Micheal Martin was speaking at an event setting out the next stages of his government’s Shared Island initiative, a year on from its launch.
The impact of Brexit and the legacy of the Troubles were both flagged as potential obstacles to reconciliation on the island.
Education, climate change and transport were highlighted as areas for greater co-operation between the administrations on both sides of the border.
“The long road of peacebuilding and the current challenges including on Brexit and dealing equitably with the legacy of the Troubles can sometimes obscure just what has been achieved since 1998,” Mr Martin said.
The initiative has seen the government focus on building new cross-border and all-island relationships, backed by millions in funding.
This has included co-operation on cross-border issues, including the Ulster Canal and the Narrow Water Bridge.
The government also arranged a series of “shared island dialogues” involving around 1,000 people, with work co-ordinated by a new Shared Island Unit.
The speech came in the same week Ireland marked 100 years since the signing of the Anglo-Irish Treaty that brought to an end the country’s war of independence against British rule.
Mr Martin said the century of marking the signing of the treaty was a reminder that a failure to resolve how people lived on the island of Ireland had often led to violence.
“We have begun to reconcile. But we must also acknowledge that 2021 has been a difficult year as we continue to grapple with the Covid pandemic, the outworkings of Brexit and dealing with the legacy of the past,” Mr Martin said.
On Brexit, the taoiseach said that the EU had been listening to unionist concerns on the contentious Northern Ireland protocol.
“We want to see an agreed outcome that works in the best way possible for the people of Northern Ireland,” he said.
“We want to finally and definitively move beyond the divisions of our past, to build together a truly shared future.”
Among the new initiatives announced yesterday, Mr Martin said that his government would be working with the Northern Ireland Executive on investment in cross-border electric vehicle charging points, as well as on a new pilot project on green hydrogen for the island’s road network.
Mr Martin also promised funding and support for climate change partnerships.