He said declining numbers of Catholic children had left schools having to fill empty places or face closure. However, he said a "balance", including a favourable number of Catholic children, was needed to ensure schools retained their distinctive ethos.
Speaking at the launch last week of a new cross-faith website for church schools in Wales, at the Millennium Centre in Cardiff, the Archbishop said:
"Single-faith schools have been attacked for not being inclusive but it's not a fair reflection of our schools today."
His comments come as some non-denominational schools continue to debate whether traditional Christian services should be removed from the school calendar. Last Christmas, some schools banned their annual nativity play because it was deemed offensive to pupils from other faiths.
A TES Cymru survey also discovered a quarter of all schools in England and Wales dropped their Christmas carol services for the same reason.
The new website, www.churchschoolswales.org, is the first joint initiative between Anglican and Catholic schools in Wales. The archbishop called for greater joint working to bridge the "historic divide" between the two religions.
Assembly officials, church leaders, teachers and union representatives attended the launch of the new website, which will service almost 300 schools and 60,000 pupils, as well as offering information and handy tips to parents, governors and the 4,000 teachers working in church schools.
A committee from Catholic and Anglican schools teamed up to compile the online resource.
The Archbishop of Wales, the Most Reverend Dr Barry Morgan, representing Anglican schools at the launch, said he was glad to see the two denominations working together.
Jane Davidson, education and lifelong learning minister, said the website was a valuable tool for church schools.