Juan Kinnear, who is in a committed same-sex relationship, was one of three people being ordained as deacon at St Paul's Cathedral. His inclusion was controversial in some quarters because there are divisions within the church on the issue of gay clergy.
During the ceremony, Bishop of Dunedin the Right Rev George Connor asked the congregation whether the deacons should be ordained.
Three people - Rev Malcolm Falloon, Rev Wally Behan and John Bryant, all of Christchurch - said they should not, and walked out.
Speaking outside the cathedral, Falloon, a member of conservative group Anglican Mainstream New Zealand, said he had hoped the interjection would provide an opportunity to present a statement to Bishop Connor protesting Kinnear's ordination.
When that opportunity did not arise, the group left quietly.
"There was no point in us continuing in the service and causing distress to the congregation," he said.
His opposition was not to Kinnear as an individual, but to Bishop Connor seeing him as a suitable candidate for deacon despite being in a same-sex relationship, he said.
Falloon said the ordination was not consistent with the rules of the church, which had from its first days insisted on marriage or celibacy for its ordained ministers.
The ordination also dismissed calls for a moratorium on the ordination of gay clergy from Anglican leaders worldwide. Most people ordained as deacons are subsequently ordained as priests after a short time.
An academic administrator at Dunedin's Knox College, Kinnear holds a bachelor of theology degree as well as masters qualifications from the universities of Natal and Waikato.
The college website describes him as having research interests in Anglican ecclesiology and canon law.
He declined to comment after his ordination yesterday.
The Dean of St Paul's Cathedral, the Very Reverend David Rice, said the interjection protesting the ordination of Kinnear was not representative of the majority view in the diocese.
The cathedral was full, and all but those three had offered support for all who were being ordained, he said.
Rice said he had received calls from other churches throughout the country supporting the ordination, and some had planned to light a candle at 1pm to mark the start of the ceremony.
The Anglican Church internationally is divided on the ordination of gay clergy, and New Zealand churches are generally regarded as being at the liberal end of the Anglican spectrum.
The Dunedin diocese has a liberal track record, having in the past welcomed a gay priest to be dean of St Paul's Cathedral and installing a woman, the Rt Rev Penny Jamieson, as its bishop. Others ordained as deacon at the ceremony were Ruth Doig of the Holy Cross Church in St Kilda, and Prue Miller of Dunedin. Roly Letham, of Dunstan, was ordained as a priest.