The first community national school opened in 2008 and the State acted as the patron.It gave the Catholic Church a commitment to provide Catholic pupils with the same programme of religious education as offered in Catholic schools.
ETBI has been engaged with separate discussions with representatives of Catholic bishops and the Department of Education, and has now decided to change its approach.
ETBI general secretary Michael Moriarty said based on a commitment to equality, it had taken the view that, "if everyone was to be treated equally, belief instruction had to be outside the school time".
Community national schools have been offering a hybrid approach to religious education - mainly a multi-belief programme for entire classes.
However, although practices varied within schools, time may also be allowed for instruction in particular faiths, if parents request it.
Patronage of the schools has now transferred to local ETBs.