Atheist Ireland says some of the proposals will make "the problem worse" rather than addressing issues
The Education Minister says the Government will push ahead with plans to divest patronage of Catholic schools.
Richard Bruton says he wants to see the process accelerated and to increase the number of multi-denominational schools to 400 within the the next 15 years.
More than 90% of the State's 3,200 primary schools are managed by the Roman Catholic Church.
The divestment process commenced by the previous Government is said to have resulted in only eight transfers so far.
The Minister is also pledging greater use of the Community National School model, and to explore the potential of different patrons in single schools.
Minister Bruton is understood to have asked his staff to work towards speeding up the divestment process, saying this is a "hugely important area".
Michael Nugent, Chairperson of Atheist Ireland, told Newstalk Breakfast that "while it seems on the surface to be addressing the problem, it's actually making the problem worse".
He explained: "What you would have under this system is 400 schools [...] that would enable some secular families to have access to some schools that are not as Catholic as others.
"But what the Catholic Church is trying to negotiate is that in return for that they will have a stronger Catholic ethos in the schools they retain - which means most families will not only not have access to schools that don't indoctrinate, but will in fact only have access to schools that have an even stronger Catholic ethos".
Mr Nugent is encouraging the Government to confine religious instruction to only the formal religion class, saying such an interim measure "would not require the State investing in anything".