The Department of Education considered cancelling State funding for school chaplains as part of recent budget cuts, but found it was not legally able to do so, according to senior officials at the Department.
It has emerged that the Department sought legal advice as to whether it could stop paying what amounts to €9m every year for the salaries of chaplains in community and comprehensive schools.
However, it was told that the payments were enshrined in the deed of trust that governs the schools and so had to continue.
The funding of salaries for school chaplains has been criticised, given the abolition of ring fenced funding for school guidance counsellors.
Speaking at the annual conference of Community and Comprehensive Schools in Killarney, Assistant General Secretary at the Department Martin Hanevy said he could not guarantee that the payments would continue indefinitely.
Mr Hanevy said the current financial situation meant everything was up for scrutiny.
The deed of trust that governs Community and Comprehensive Schools is currently being revised.
He declined to rule out a suggestion that the issue of the State payment of school chaplains could be "unhooked" as part of this revision.
Separately, an Evangelical church and a Muslim patron body are among applicants to open new secondary schools in Ireland.
The Department of Education has received almost 30 applications for patronage of 14 proposed new second level schools, which are due to open in 2013 and 2014.
The list of applicants has now been published on the Department's website.
The Redeemed Christian Church of God has applied as patron of a new school planned for Navan in Co Meath.
The Muslim Primary Education Board has applied to open a school in Blanchardstown in Dublin.
Other applicants include the VECs, Educate-Together, as well as Catholic religious trusts.
The Department said it hopes decisions on the four schools due to open in 2013 will be made by late June or early July.
The conference in Killarney is focusing on the issue of patronage in schools.