The Presbyterian Moderator Harry Uprichard has declined an invitation to attend an inter-denominational service.
Moderator Harry Uprichard has difficulties with interchurch services
The service, scheduled for the first Sunday in June, is held to mark the annual RUC George Cross Day.
Dr Uprichard said his decision was taken "simply and purely" on the grounds of personal conscience regarding joint worship.
"We are allowed that option as moderator and the church is being represented," he said.
"I am more than happy and more than encouraged to support the work of the RUC whatever the religious affiliations of those connected with it are."
The Moderator said he appreciated "totally, completely and absolutely, the fine work that has been done and is being done in that particular aspect".
"My concern is that the involvement of inter-church worship to that degree publicly aligns those of the reformed faith with those not of the reformed faith," he said.
Dr Uprichard said there were "insuperable difficulties" connected to interfaith worship and he felt it was "incorrect to be so aligned under those circumstances".
"There are deep fundamental differences," he said.
"I respect those who disagree with me, I respect their opinion but I disagree with it, feel I must agree to disagree and that puts me in the position where I can't be party to involvement."
The church's press officer, Stephen Lynas, said that "from time to time" moderators would be prepared to involve themselves in inter-church services.
"Consequently, we then are represented by a former moderator who is prepared to represent our church in those circumstances," Mr Lynas said.
The Presbyterian Church in Ireland has about 300,000 members in over 560 congregations and is the largest Protestant denomination in Northern Ireland.
Dr Uprichard ends his term as moderator in June. Reverend David Clarke of Terrace Row Church in Coleraine will take over.