Archbishop Peter Jensen has publicly disagreed with former Prime Minister Kevin Rudd, who has done a turnaround and now says he supports same sex marriage.
Dr Jensen says Mr Rudd's comments "do not grapple sufficiently with the question of what marriage is and what it is for".
In a blog post on his electorate website, Mr Rudd said that after a conversation with a political staffer who he described as a pentecostal 'god botherer' he came to the conclusion that "church and state can have different positions and practices on the question of same sex marriage".
Although disagreeing with the christian viewpoint that homosexuality was wrong, as would be same-sex marriage, Mr Rudd said "I believe that this change should legally exempt religious institutions from any requirement to change their historic position and practice that marriage is exclusively between a man and a woman".
Prime Minister Gillard and Opposition Leader Abbott maintain their positions against same-sex marriage.
Dr Jensen told the Australian newspaper "I respect Mr Rudd and have always enjoyed my conversations with him on all sorts of subjects. He is an interesting and thoughtful man. On this matter, however, I am unconvinced."
The Archbishop said "His discussion of the bible is historically shallow and he may be too confident about the state of current research" - referring to claims by Mr Rudd that children in same-sex relationships suffer no disadvantage.
But Dr Jensen said the main issue was that the statement and thinking outlined by Mr Rudd did not fully grapple with marriage and its intention.
"Equality is not the issue. The consummation of a marriage by a man and a woman is unique and cannot be replicated. The precious differences between men and women, likewise cannot be replicated in any other bond".
Dr Jensen went on to tell the newspaper "Marriage is too important for all of us - it is not a church-state issue - to redefine it for the sake of an illusory equality. What cannot be done should not be attempted".
Muslim and Jewish leaders quoted by the newspaper also supported the institution of marriage as between a man and a woman.