Richard Bruton says the new arrangements mean students will no longer be "sitting at the back of the class"
Multi-denominational secondary schools have been warned they have to offer students something to do during religion classes if they opt out.
A circular has been issued by the Department of Education to say they will have to provide alternative tuition throughout the school year rather than supervised study.
The new arrangements take effect immediately, and apply to both education & training board (ETB) and community secondary schools.
As well as religious instruction, the circular also covers religious worship - such as masses held during the school day.
The department says it is 'no longer an appropriate approach' to assume that the student population is predominantly Catholic.
Parents, meanwhile, will no longer have to request a withdrawal from religious instruction, with officials saying the wishes of parents "will have to be established as part of the process for planning and organising of subject selection".
Education Minister Richard Bruton says he does not want any pupils left "sitting at the back of the class or confined to the library".
He explained: “It is important that ETB and community post primary schools as multi-denominational schools, fully implement this circular as it presents an important opportunity to meet the expectations of parents and students in a changing society.
"This can only be achieved by consulting with parents, and including their wishes as part of the normal planning process of any school."
While the new guidelines take immediate effect, the department also says it accepts that revised timetables reflecting the rules may not be feasible until the start of the next school year.
The new arrangements, however, do not apply to religious-run schools.