A report for the Church in Wales says children who attend its primary schools are consistently doing better than children at other schools. The decision to publish the findings has angered some headteachers.
The Church in Wales says pupils at its primary schools do better than the average for children at other schools.
A review looking at pupil achievement at 168 Church in Wales primary schools found they were consistently above the average in English, maths and science.
The Church in Wales said it believed in the importance of education, not religious or a church school education.
The Welsh Assembly Government said it would "carefully consider" the findings of the review.
The Church in Wales's education review looked at the achievement of more than 20,000 Key Stage Two pupils across Wales, seven-to-11 year olds, in what it said were the core subjects of English, maths and science.
The review, the first undertaken by the church, challenges claims that faith-based education is selective.
Mark Durbin, head of Henllys Primary School, Cwmbran
"We have a strong ethos at the school where everyone is at the centre of their own personal development. Children are encouraged to work well with each other. The Christian belief of caring for one another means that everyone is valued.
"Church schools are also seen as very strong family schools. It's very much a triangle where we have the parents, the church and the school with the children at the centre of that triangle.
"Also within church schools you usually get a very low turnover in staff where staff share that ethos and feel welcome in that family atmosphere. I think that leads to continuity and progression within the school."
Henllys is a Church in Wales school attended by around 220 pupils
The church said the study found that almost 80% of Church in Wales schools serve the children in their locality without regard to their parents' faith position.
Of the remaining 20%, the church claims its review found "positive, mixed-school communities" which were "diverse in their intake and outlook".
The review highlighted the contribution of parish clergy, showing that three-quarters of them were involved in their local schools.
It also emphasised the need for good religious education and for collective worship.
'Context is key'
The Archbishop of Wales, Dr Barry Morgan, said: "This review clearly shows how schools with a strong Christian ethos nurture and encourage our children and help give them the best possible start in life.
"That is why Church in Wales schools are successful and why there is a strong demand for places at them.
"We commissioned the review because we are committed to education and want to continue working, alongside the Welsh [Assembly] Government, to ensure these high standards are maintained and as many pupils as possible are able to benefit."
The report is to be launched at a meeting of the Church in Wales' Governing Body at the University of Wales, Lampeter.
Anna Brychan, director of the head teachers' union NAHT Cymru, congratulated the Church in Wales for the result of its schools review, adding that many of the church primaries were led by her members.
She said: "The only fair way of evaluating how schools are doing is to consider them in their context. Context is key here.
"If you just compare all faith schools against the mean, that won't give a necessarily full picture of how individual schools perform in their communities.
"I would urge parents when choosing a school for their children to look at what schools offer, including faith-based schools, but to consider their achievement in the context of their communities."
Ms Brychan added that the importance of a school's ethos was "more widely recognised than just the faith-based sector".
Some experts say many church schools are in rural or affluent areas and are well supported by parents.
Others argue strong pastoral support at faith-based schools could provide a credible explanation for the results.
A Welsh Assembly Government spokesperson said it welcomed the report of the review group.
"We will carefully consider those recommendations that apply to the Welsh Assembly Government and respond in due course, however, we are focused on supporting learners in all settings to ensure that all pupils reach their potential in Wales."
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