The Higher Education Authority has expressed concern about the appropriateness of chaplaincy arrangements in some of the country's third-level institutions.
In a review of chaplaincy services carried out by the HEA it says the predominance of Catholic chaplains makes it critical that institutions ensure all students have access to the same level of service regardless of faith.
The review was commissioned last year by the then minister for education after concerns were raised about this predominance, and the fact that many third-level chaplains are appointed directly by the Catholic Church.
Chaplains provide a number of supports to students, including counselling and assistance with accessing financial support.
The HEA has recommended that all institutions ensure that chaplaincy and other support services are available to students of all faiths "in keeping with their responsibilities under the Irish constitution".
It says the use of lay chaplains could be considered as a means to address that.
It says any institutions with "legacy" arrangements in place that did not involve a formal process of appointment or procurement in line with public sector rules should seek to do so within the next 12 months.
Documents received by the organisation Atheist Ireland from the HEA last year showed that in the case of Cork Institute of Technology, the Bishop of Cork and Ross nominated a candidate who was then employed by the college on an Assistant Lecturer grade, with an annual salary of €66,000.
Other colleges had similar arrangements.
The documents showed that CIT paid half the cost of repainting the house in which the chaplain, a Catholic priest, lives and works.
Freedom of Information responses showed that in many colleges, the position of chaplain was not advertised publicly, and there were no records of any interview process or any decisions related to the appointments.
The salaries and costs associated with chaplaincies come generally from the overall State funding provided to the institutions.
However, in the case of the Institute of Technology in Tallaght, Limerick IT, and IT Tralee, students pay for the service through their fees.
Atheist Ireland says the HEA review has vindicated its stance.
The organisation says the HEA recommendations introduce a requirement that these public positions will no longer be reserved for male priests, appointed at the discretion of bishops.
It says it believes that any suitably qualified candidate, of any faith or gender, will now be able to apply for "these important roles".