The Most Rev Glenn Davies urged voters to oppose plans to allow same-sex couples to wed when a voluntary postal vote is held next month.
The country's most senior Anglican leader said: "We know from recent experiences in the United Kingdom and North America that the ramifications of such a change are profound.
"Their experience shows us that if the law is changed, it will have direct impact on people of faith and faith-based institutions."
Archbishop Glenn said his stance "is not a homophobic reaction" but about recognising "God's plan". He also said that "retaining the (current) definition of marriage is best for our society".
In an open letter, he went on to say: "As Christians we know it (heterosexual marriage) is God's plan; but it is God's plan for humanity, not just the people of God.
"It is the best structure for society and for the procreation of children in the secure nurture of a family with a mother and a father."
Thursday was the last day for Australian citizens to register to vote in the postal survey. The Australian Electoral Commission revealed 50,000 people had signed up since the vote was announced a fortnight ago.
Archbishop Glenn voiced concern that the legalisation of gay marriage could see Christians who oppose the idea losing some of their rights in the workplace.
He continued: "Despite the claims of some, that religious freedom will be protected, all proposed legislation to date has been totally inadequate to safeguard people who work for church-run institutions such as schools, hospitals and universities.
"It is also unclear whether church-based organisations will be free to employ staff who share their church's teachings and ethos.
"In some countries where marriage has been redefined, schools are prevented from teaching that marriage is between a man and a woman, even in faith-based schools."