The Anglican Church's ruling body this month issued an apology to the gay, lesbian, bisexual and transgender community. It also told clergy they could bless same sex marriages with a bishop's permission and set out a path to formalising the recognition.

The Herald is aware of intense debate in congregations grappling with how to accept the ruling of the governing body, the General Synod.

Mr Hughes said he knew of other churches in which rifts had formed.

"There is a large body of Anglican clergy who are convinced this is the wrong way to go."

There was also a group of lawyers — including two QCs — who were working on a legal challenge to the church's move.

Two-thirds of St Michael's board had also resigned as had half the staff, while Mr Hughes was in talks with a non-Anglican church to take over as minister.

He said he would welcome his former parishioners if they chose to join the new congregation.

He said in his view there was an inconsistency between same sex relationships and membership of a Christian church.

Mr. Hughes said the Bible was explicit in its opposition to sexual acts between people of the same gender.

"I, in no way, support repressive policies against homosexuals," he added.

"I am prepared to be supportive and engaged with people who experience same sex attraction but I cannot approve of those who participate in same sex acts."

He said there would be a "tension between living according to the Bible and the lifestyle choice they make".

The Bishop of Auckland the Very Reverend Ross Bay told St Michael's parishioners that he understood there would be "confusion and even anger" over the situation.

He said Mr Hughes had spoken of making a decision of conscience.

"I respect his decision and so have accepted the inevitable consequence that his licence as vicar must lapse as a result."

He also said the church's position had not changed, with work under way to develop ways in which clergy opposed to same sex marriage did not have to bless the relationships.

A new priest would be appointed.

Labour's Louisa Wall, who championed same-sex marriage legislation through Parliament, welcomed the Anglican Church's move to take a position across its parishes.

"It says to me the Anglican Church has always been the most progressive."

Church rules

• The Anglican Church's General Synod set a two-year deadline in which formal rules would be developed for a religious ceremony blessing same sex relationships - and a structure relieving opposing clergy from being made to do it.

• The Synod also allowed clergy to seek the approval of their bishop to recognise same sex marriages among parishioners — although clearly stated "such recognition cannot be marriage".

• The Synod apologised to the LGBT community, saying it had "too often ... been complicit in homophobic thinking" and had "failed to speak out against hatred and violence against those with same-gender attraction".

David Fisher is a senior reporter for the NZ Herald