In a letter to Australian bishops Most Rev Phillip Freier said: "Individual Anglicans have adopted a variety of positions taken in good conscience based on their Christian understanding of the principles and issues, and this is right and proper."
He went on: "Should the vote be in favour of same-sex marriage as suggested by the opinion polls, the Church must accept that this is now part of the landscape.
"We can still stand for and offer holy matrimony between a man and a woman as a sacred ordinance given by God, while accepting that the state has endorsed a wider view of marriage."
Most Rev Freier's words come as the Anglican Communion is experiencing significant division over the issue of homosexuality.
Recently a conservative wing of the Church, GAFCON, said it would "warmly commend" a split if it meant protecting what they say are traditional biblical teaching on the issue.
Meanwhile 131 Church of England clergy and laity wrote a letter to bishops urging them to be "unequivocal" in their recognising LGBT (lesbian, gay, bisexual and transgender) people as "essential to the health and future" of the institution.
A date for a referendum on same-sex marriage in Australia has not yet been confirmed.