Taoiseach Leo Varadkar has said Brexit concerns are partly responsible for the powersharing impasse at Stormont.
The two largest parties in Northern Ireland, Sinn Féin and the DUP, are on opposing sides over the Britain’s exit from the EU.
Sinn Féin has called for a new referendum on Irish unity within five years amid nationalist hopes the exit could inspire greater support for a united Ireland.
Mr Varadkar said he was resolutely committed to protecting the peace process across Ireland.
He said: "We don't want things going backwards.
"We have to acknowledge that the continued absence of functioning political institutions in Northern Ireland is, at least partly, a consequence of concerns about, and different positions on, Brexit."
The Taoiseach addressed a conference in Dundalk, Co Louth, where EU chief negotiator Michel Barnier warned that Brexit talks were at risk over the border issue.
Mr Varadkar acknowledged some unionists were worried that Brexit could be used to undermine Northern Ireland's union with Britain.
He said: "I want to repeat that we have no hidden agenda.
"Our agenda is fully transparent - it is respect for the primacy of the Good Friday Agreement and everything it represents for the people of these islands.
"That includes the principle of consent, peaceful politics, democratic institutions, reconciliation and cooperation."
Stormont powersharing has been suspended for more than a year.
It collapsed in a row over the DUP's handling of a botched green energy scheme, but quickly escalated into a dispute over identity, with calls for official protection for the Irish language a sticking point to return of the devolved institutions.
Mr Varadkar added: "I am determined to work with the British government, with the political parties in Northern Ireland, with the unionist and nationalist communities to chart a way ahead.
"We want to see all parts of the Agreement operating and I also want to see the great strides that we have made on North/South cooperation continue and grow in the years ahead."