No additional resources will be given to State secondary schools so that students who opt out of religion can study something else.
Teachers and school managers say a lack of extra teachers threatens to jeopardise the changes aimed at reflecting a decrease in religious belief and practice among students.
Until now, many students in secondary schools run by Education and Training Boards (ETBs) who did not want to participate in religious instruction or worship were forced to sit at the back of the class.
A new Department of Education circular will change this practice by obliging schools to consult with parents – or pupils over the age of 18 – over the option of studying alternative subjects.
Minister for Education Richard Bruton said schools will have to "reconfigure their resources" as best they can to serve the needs of students opting out of religion classes.
"They have to reconfigure their timetable so children who don't want to participate in religion get the opportunity to do other things. That is common enough at second level where there will be students doing different options," he told RTÉ Radio 1's Today with Sean O'Rourke.
The Teachers' Union of Ireland, however, said it had "serious concerns" over the failure of the Minister to provide resources for this measure.
“On a practical level, other subject options will have to be provided at the time that religion takes place. Quite clearly, this will require the employment of additional teachers in schools,” the union said.
Education and Training Boards Ireland (ETBI), the umbrella body for State schools, described the move as a “step in the right direction”, but also sounded caution about resource implications.