New Zealand's Anglican Church will bless same-sex relationships after a landmark vote this morning.

The Anglican Church in Aotearoa, New Zealand and Polynesia stopped short of permitting gay marriages in church but will allow ministers to bless couples in same-sex civil marriages or civil unions.

The motion, debated at the biannual synod in New Plymouth this week, means bishops can either allow or deny priests in their diocese permission to bless gay couples in committed relationships.

The Anglican Church in Aotearoa, New Zealand and Polynesia consists of three tikanga, or partners; Maori, Pasifika (Polynesian) and Pakeha (European). The issues has been debated among all three for almost 50 years.

Wednesday's motion was strongly opposed by the Pasifika, or Polynesian, group which said the move would not be accepted in the Pacific islands.

However they abstained from the vote and did not vote against it so as not to restrict their Tikanga Māori and Tikanga Pākehā partners. The motion easily passed.

The Pasifika churches, along with other conservative churches, will opt out of the change with the motion designed to appease conservative opponents. Rather than forming official liturgy, and so part of the church's teaching, the blessings will not be written and instead will be given more informally, the motion said. This was designed to try and hold together the opposing sides,

However the result prompted immediate resignations from two prominent conservatives.

Rev Jay Behan, chair of the traditionalist Fellowship of Confessing Anglicans New Zealand group and member of the ruling synod, wrote to the three archbishops and other members to announce he would quit.

'The passing of this report finds us left behind and unable to move forward with you in good conscience as we seek to honour the Lord and love His people,' he said in a letter also signed by another conservative, Rev Al Drye.

'We leave with no anger or bitterness in our hearts and we wish you the best as you seek to serve the Lord Jesus Christ.'

In a statement the Fellowship of Confessing Anglicans New Zealand said: 'While we are thankful for the gracious spirit in which the debate was held, we disagree with the final outcome. We believe the General Synod has acted in a way which leaves behind biblical authority, the apostolic tradition, and the doctrine and practice our church has always held.'

It added that it was ready to welcome other conservatives who opposed the decision.

'FCANZ believes that God loves all people, from all walks of life, calling each of us to repent and have faith in Jesus Christ. Sometimes speaking of this love involves saying difficult things that run counter to the culture of today. However we remain convinced that it is good for all humanity and the only place for the church to stand.'

But Very Rev Ian Render, who is dean of Waiapu Cathedral and also gay and married, said in the debate: 'I'm standing to remind you of all the people we have lost along the way. The people who were candidates for ordination – but who were turned down because of their relationships, or their declared sexuality.

'The people who have been left in limbo, for year, after year, after year.

I would like, in this late stage of my stipended ministry life, to feel as though I – and everyone else like me – finally will have a place to stand in this church.

'Thank you for the graciousness that I have experienced in these past couple of days. Please give me, and others, a place to stand.'