The Church in Wales' first ever Education Review found its 168 schools' overall performance to be "consistently above the average" for the country.
Responding to the report's release, the Welsh Assembly Government said it will "carefully consider" its findings.
A government spokesperson said it welcomed the research, adding: "However, we are focused on supporting learners in all settings to ensure that all pupils reach their potential in Wales."
Some commentators, including Anna Brychan, director of the head teachers' union NAHT Cymru, stressed the importance of context and warned against like-for-like comparisons.
The review examined the achievement of more than 20,000 seven to 11-year-olds in what it described as the core subjects of maths, English and science.
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."
Written by Charlotte Michaels