Simon Harris chose not to attend the annual Remembrance Sunday commemoration at Enniskillen on advice from his “most senior officials”.
Mr Harris’s absence will represent a notable break with the tradition of the sitting Taoiseach attending the event.
The commemoration falls two days after he formally announced an election in Ireland.
Speaking to reporters on Saturday, he explained that officials said the attendance of the Taoiseach was based on the presence of members of the Northern Ireland Executive.
Mr Harris said: “This was on official advice from the most senior officials in my department because there isn’t – I don’t believe – a representative from the Northern Ireland Executive attending which is when the Taoiseach of the day – whoever he or she is – would usually attend too.”
Mr Harris said the Government would be represented at “senior level” by his Fine Gael colleague and cabinet minister Heather Humphreys.
It represents a significant break in a tradition begun by Enda Kenny.
Mr Kenny became the first taoiseach to attend a Remembrance Day service in Northern Ireland when he took part in commemorations at Enniskillen in 2012, in a move seen as symbolic of greater recognition afforded in the Republic of Ireland to Irishmen who fought and died serving in the British Army in the First World War.
His attendance also marked the 25th anniversary of an IRA bombing at the memorial in 1987.
The tradition has been followed almost every year since Mr Kenny placed a laurel wreath at the base of the memorial.
Eleven people who had gathered to pay their respects to the war dead were killed and dozens injured in the no-warning blast on November 8 1987, minutes before the Remembrance Sunday ceremony was due to start.
A 12th victim of the Poppy Day bombing died 13 years later having never woken from a coma.
Mr Harris’s decision to miss the event was criticised by the South East Fermanagh Foundation (SEFF), a victims’ group which works with many of the families affected by the bombing.
It called on him to engage with the bereaved families after the election.
Asked about the request, Mr Harris said: “Certainly, I very much want to and am happy to engage with the families.”
