The Reverend David Lord – a former Hamilton emergency room doctor ordained as a deacon in December 2005 – angered conservative Christians by exchanging rings and vows with his partner in a church ceremony for his civil partnership in London last month.
But Dr Lord, who tied the knot with English clergyman Peter Cowell, a hospital chaplain, "felt it appropriate to lay down his clergy licence", according to a statement jointly released with the Bishop of Waikato, Rt Rev David Moxon.
His decision will bar him from officiating as a priest.
Dr Lord and Bishop Moxon declined further comment.
At the time of his ordination, Dr Lord said his religious faith had been deepened at university with the acknowledgment that his vocation as a doctor was a humanitarian calling from God.
A spokesman for the Anglican Church said neither Bishop Moxon nor his London counterpart were told in advance of the wedding celebration. The Anglican canon on marriage spoke only in terms of traditional marriage.
"As the rules stand, there is no rite of blessing in the canon for same gender couples."
The Telegraph newspaper reported that Dr Lord has already returned to New Zealand and that Rev Cowell, the chaplain at London's St Bartholomew's Hospital, plans to follow him out here.
The couple's elaborate wedding ceremony at the historic St Bartholomew the Great church in London has incensed a breakaway Christian group, unhappy with the liberal agenda of western churches, which is due to meet next weekend in Jordan to decide whether it can still retain links with the Anglican communion.
The Times newspaper said that one view of the ceremony was that the traditional liturgy used was deeply provocative.
Much of the anger toward the couple came after details of the service were revealed. Traditionalists were angry that the men were able to enjoy a ceremony almost identical to a traditional church wedding, with readings, hymns, a Eucharist and a version of the 1662 Book of Common Prayer's Solemnisation of Marriage.
Conservatives in the church, especially from Africa, accused the couple of undermining the authority of the Bible and the sanctity of marriage.
The Telegraph reported that Britain's first church ceremony for a homosexual couple means that conservative factions are now more likely than ever to claim the Communion has been irreversibly split. Some traditionalists may even say they must formally sever links with the Archbishop of Canterbury and form a new "orthodox" church.
The Rev Martin Dudley, who led the service, downplayed the event's political significance:
"I am surprised and disappointed by the fuss. It was a joyful, godly occasion. Why turn it into a controversy? It was not a rally or a demonstration," he said.
It was not the first time there had been prayers, hymns or readings following a civil partnership, though he conceded: "It may be that this ceremony had rather more knobs on," The Times reported.
Liberals reacted with disappointment to the news of Dr Lord's resignation.
The Rev Dr Giles Fraser, vicar of Putney and president of Inclusive Church, a campaign group working for equal rights for gay Christians, said: "This is disgraceful. It's amazing this church cannot celebrate what little love there is in this world. It was supposed to be the happiest day of their lives and they have been turned into outcasts."
Others said they hoped the gay ceremony would help the church modernise. The Rev Richard Kirker, chief executive of the Lesbian and Gay Christian Movement, said: "I hope it nudges the church into the 21st century. There are so many gay clergy in civil partnerships, whose integrity leads them to wanting to have their relationships affirmed by their faith."
