Some private Christian schools are singing an alternative version of the national anthem which promotes religious values and talks of Christ.
Instead of the official second verse of Advance Australia Fair, which starts "Beneath our radiant Southern Cross", the alternative verse says "With Christ our head and cornerstone, we'll build our nation's might".
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The version of the anthem is sung every fortnight at Thornlie Christian College and Christian Schools Australia WA executive officer Ray Dallin confirmed that it was regularly sung at other school assemblies and churches.
He believed the verse was in the original anthem by Peter Dodds McCormick but had been omitted from the official version.
"It's probably normal for the Christian schools to do that because it's the Christian element of that song which is often left out," he said.
But others say the existence of a missing Christian verse is a myth started by Awakening, a Christian movement, and it was never part of the composer's original work.
Original verses from 1879 in the National Library of Australia music collection do not include the Christian verse.
A spokeswoman from the office of Prime Minister Julia Gillard said that under national protocols, the anthem should not be modified and alternative words should not be used. The two authorised verses were proclaimed in 1984.
Thornlie Christian College principal Bill Innes said the extra verse had been in use at the school since he started there nine years ago.
"If it was offensive to our community I would certainly look at taking it away," he said.
"We are about honouring our country and that is why we make a point of singing the anthem at every assembly."
Mr Innes said he had assumed it was an official verse.
Association of Independent Schools of WA executive director Valerie Gould said it was up to individual schools to decide what was sung at school assemblies.
Shadow education minister Ben Wyatt said it was important that all students learned both verses of the original song. "The school should make it clear it's the school's version of the national anthem, not the official version," he said.
WA Returned and Services League president Bill Gaynor said any words used in the national song should be of a patriotic nature and embrace themes that are a cornerstone of Australian society.
"And Christianity is one of the cornerstones of our society," he said. "I think anything that reflects that would be appropriate."