Minister for Education Richard Bruton has said his department will pursue schools that are refusing to implement new regulations governing the teaching of Religion at post-primary level.
Almost half of the country's post-primary schools have ignored a directive from the department that they offer students who do not wish to do religion the choice of an alternative subject.
The order, issued last February, applied to all state-run second level schools. These are schools run fully or partially by local ETB or Education and Training boards.
The schools were obliged to implement the directive by this academic year, but they have not done so.
Mr Bruton has said that the new rule, like every other one, "has to be honoured".
He said department inspectors would inspect schools to make sure that the directive was respected.
Mr Bruton said it was very important that multi-denominational ETB schools fulfilled the principal under which they had been established, and that meant accommodating those of religious faith and of none equally.
He insisted that those schools had to respect their responsibilities, and said the department would "be pursuing whatever avenues we need to ensure that schools respect what is required".
Education and Training Boards Ireland, which represents the country's 16 ETBs, has told RTÉ News that it has "sought clarification" on the implementation of the new regulations and that schools in the sector "will maintain the status-quo in relation to the provision of Religious Education and opting out until clarification is received".
In a statement it said that once clarifications were received the implications "will be considered".
School students have a constitutional right to opt out of religious education if they wish to.
However the practice in the vast majority of schools, including state-run multi-denominational schools, is that students in this position are obliged to remain in the classroom while the religious education class takes place.
The new rules, issued last February, oblige schools to consult with parents as to whether or not they wish their child to participate in religious education.
They state that this should be done as part of the overall process of students making their general subject choices.
They oblige schools to offer an alternative subject to students who do not wish to do Religion.
The rules apply to all Community and ETB (formerly VEC) schools, which comprise almost half of all post-primary schools in the country.
Teacher unions were among those who objected to the rules when they were published last February.
They argued that schools did not have the resources to implement the directive.
The Catholic church also objected.
It is highly unusual for a schools' sector to not implement a directive from the Department.