State-run secondary schools are failing to provide students who opt out of religion access to another subject.
The Department of Education told schools, such as community schools or ETB schools (run by Education and Training Boards), last year they must provide an alternative for students on their timetables.
These types of schools make up around half of the country's secondary schools.
The Irish Times reports that most State schools are unable to meet the requirement because of a lack of resources.
Chairperson of Atheist Ireland Michael Nugent said it is a shocking situation.
Mr Nugent said: "These are the Education Training Board (ETB) schools, so the old vocational training schools. They are supposed to be the alternative to religious denomination schools and meant to reflect the entire community.
"Now the Department has recently told them they have to stop doing that."
Nessa White, general secretary of Education and Training Boards Ireland, confirmed that a circular from the body in charge of ETB schools told them to “maintain the status quo in relation to the provision of religious education and opting-out arrangements”.
Ms White said: “Religious education is open to all students regardless of their religion or world view.
"In some instances, parents or students over the age of 18 wish to opt out of religious education. This is fully permitted in ETB schools.
“However, our schools have not been provided with any additional resources to provide alternative classes to students who opt out. Our schools cater for these students to the best of their ability with the resources currently available to them.”