In response to complaints of parents, the Edgewater Primary School in Perth's north has banned the recitation of the Lord's Prayer.

The basis of the prohibition, which ended a practice of 25 years, was the Western Australia Education Act, which says schools may not favour one religion over another.

The students used to say the prayer at the start of each fortnightly assembly. Edgewater Principal Julie Tombs wrote a letter to the parents Monday to inform them of the policy change. She said most parents want to carry the tradition, but only 36 per cent of them replied to a survey the school conducted to get their views about the Christian prayer.

"We acknowledge that of the parents who did respond to the survey, many wanted to retain the Lord's Prayer and it is right that we continue it at culturally appropriate times such as Christmas and Easter, as part of our educational program," Tombs said in a statement.

The principal added Edgewater students would continue to recite the school creed, which has a reference to God.

Western Australia Premier Colin Barnett accepted the decision.

"My own view is that WA is basically a Christian-based community and I think it's desirable to have the Lord's Prayer said.... (But) that decision rests at the school level. Certainly schools can, and I would encourage them to have the Lord's Prayer," he told AAP.

"I don't think it offends anyone; it just simple reflects the values and backbone of our society," the premier added.

The Anglican dean of Perth, John Shepherd, shared the premier's views.

"I think there is a place [for the Lord's Prayer], just as there is a place for exposing children to the full knowledge of other faiths," he told The Sydney Morning Herald.

Western Australia is made up of 23 per cent Roman Catholics, 28 per cent Anglicans and the remaining 49 per cent made up of followers of other Christian denominations, Buddhism, Islam, Hinduism, Judaism and nonbelievers as well.