A popular Wellington church will defy the Presbyterian Church's decree and will continue to perform same-sex marriages.

The General Assembly of the Presbyterian Church of Aotearoa New Zealand decided yesterday to ban its ministers from conducting same sex-marriage ceremonies.

Wellington's St Andrew's on The Terrace had opposed the decision, Reverend Jim Cunningham said.

"Although 150 voted for the ban there were 50 people against it and about 100 people walked out and refused to vote, this isn't the way to deal with this."

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Sexual orientation did not matter, Rev Cunningham said.

"What matters in a marriage is the quality of the commitment and the love they have for one another and at St Andrew's we will continue to help couples of the same or opposite sex who want to get married to do that and celebrate their love."

Since last year the church had been conducting same-sex marriage, and he was saddened the church had acted in a way that rejected people who seemed to be on the margins, Rev Cunningham said.

"If people have a love for one another and they are willing to make that commitment, I am willing to help them do that."

Presbyterian Church of Aotearoa New Zealand General Assembly Moderator the Right Reverend Andrew Norton said the motion was moved for the sake of clarity, but said he would prefer for the process to continue in conversation rather than making it a legislative process.

"We had our statement that marriage is between a man and a woman in a loving and faithful relationship.

"The movers of this motion believed that that was not clear enough, in other words could a minister marry a same sex couple, that was the question."

If St Andrew's church did not comply with the assembly's decision, disciplinary action would be taken, however, Rev Andrew Norton would not confirm what kind of action.

"If a church chose not to respect this then there would need to be a complaint laid and the church has it's own disciplinary processes it would fall into."

However, gay couples were absolutely welcome to attend the church, he said.

Rev Cunningham said ministers at St Andrew's had been blessing same-sex relationships for over 20 years and when it was possible for couples to have a civil union they conducted them too.

"This is a place where we tend to be at the forefront of trying to confront issues of injustice, and the attitude of the church is mistaken in terms of gay people."