The vote on Thursday sets up a showdown next month as global Anglican leaders, including the Scottish and Australian leaders, will gather in Canterbury for the second time in less than two years.

Archbishop Freier faces a tense encounter with his Scottish counterpart at a primates meeting in Canterbury next month.Reuters

It comes after the SEC voted to remove the teaching that marriage was between 'one man and one woman', leaving the door open for priests who wanted to conduct same-sex weddings.

The move has deepened divides within the worldwide Anglican Communion but the Australian Church's decision to publicly criticise it will further heighten tensions.

Its synod approved a motion that 'notes with regret' the decision to change the teaching on marriage and says: 'This step is contrary to the doctrine of our Church and the teaching of Christ that, in marriage, "a man will leave his father and mother and be united to his wife, and the two will become one flesh".'

It goes on to express 'our support for those Anglicans who have left or will need to leave the Scottish Episcopal Church because of its redefinition of marriage and those who struggle and remain'.

The text of the motion was altered several times throughout the debate, eventually becoming more hardline than the initial statement. The final version received widespread support across the three 'houses', passing by 60 to 45 votes among the laity, 68 to 42 votes among the clergy and 12 to six votes among the bishops.

Australian's primate, the Archbishop of Melbourne Philip Freier, will meet the Scottish Primus, the Bishop of Moray, Ross and Caithness Mark Strange, along with the leaders of the other 39 Anglican provinces around the world next month.

Hinting at a potentially tense encounter between the two leaders, the motion concludes by praying 'that the Scottish Episcopal Church will return to the doctrine of Christ in this matter and that impaired relationships will be restored'.

The SEC's decision to allow gay marriage in church was widely celebrated among more liberal leaning Anglicans around the world but has prompted retaliatory action from conservatives.

The traditionalist network GAFCON appointed Andy Lines as a 'missionary bishop' for Europe in response, saying he will offer alternative oversight to Anglicans who no longer feel they can come under the authority of their official bishop.

Two conservative leaders have refused the Archbishop of Canterbury's invitation to Canterbury next month on the basis of the SEC's decision.

The Archbishop of Uganda, Stanley Ntagali was joined by the influential Archbishop of Nigeria Nicholas Okoh who hinted at a split when he snubbed Justin Welby's invitation earlier this week, warning the Church was 'in the midst of the next great Reformation'.

'Everything else is the same or worse,' Okoh wrote comparing Welby's tenure to that of his predecessor Rowan Williams. 'There is endless debate, the will of the orthodox Primates is frustrated and misrepresented, false teaching is not being corrected, and nothing is being done to halt orthodox Anglicans in North America (and maybe soon elsewhere) being stripped of the churches that have helped form their spiritual lives.

'In these circumstances, I have concluded that attendance at Canterbury would be to give credibility to a pattern of behaviour which is allowing great damage to be done to global Anglican witness and unity.'