Some of the nation's Presbyterian churches are revolting against a ban on performing same-sex marriages imposed by their national body.

Last year, the Presbyterian Church of Aotearoa New Zealand (PCANZ) banned its ministers from performing same-sex marriages after the issue was put forward to the general assembly by a regional presbytery.

PCANZ moderator Right Reverend Andrew Norton said the assembly decided "ministers may conduct marriage only between a man and woman".

"While the rule came into effect immediately [in October 2014], general assembly decided to adopt the rule 'ad interim', which means that the decision requires discernment and ratification by local churches and our regional church bodies," Mr Norton said.

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Presbyterian churches around New Zealand have until October 10 to submit a response from their local church.

Reverend Doug Lendrum, of St David's Presbyterian Church in Auckland, said his church did not support the assembly's ban.

"The decision of the assembly was made, our congregation was noted as dissenting the motion," he said.

Mr Lendrum surmised performing same-sex marriages could be in St David's future, as supporting same-sex marriage had been "the stance of this congregation for a number of years".

St John's in the City is one of a number of Presbyterian churches in Wellington that do not support the ban.

St John's minister Reverend Allister Lane said the congregation was against the ban because it didn't reflect its views.

"We simply feel it's a divisive issue for our church, and therefore to come down one way or the other we can't find ourselves supporting a divisive decision," Mr Lane said.

With the ratification process ending in October this year, the general assembly is expected to announce a permanent outcome at its 2016 meeting.

Mr Lane said the ruling did not reflect the wider Presbyterian Church well.

"I think that the decision is difficult when there's a spread of opinions and if a decision lands one way or the other, it doesn't allow for those different positions to be held. It basically ignores the full spectrum of views that are faithfully held."

Mr Lane said the assembly would have to reassess its position if there was a majority of support from church councils for same-sex marriage.

"If the majority of church councils say, 'yes, that's fine', then the decision is binding, but if they say, 'no we disagree with this decision', as St John's have, then they would have to drop that decision."

Despite disagreeing with the assembly, Mr Lane said his church had no plans to marry same-sex couples in the near future.

"We think that the decision is a problem, but we're not taking up the contrary view either."

St John's was one of many churches in Wellington that felt uneasy about the ban.

Khandallah Presbyterian Church Reverend Ryhan Prasad said his church "enthusiastically disagree" as well.

"Khandallah is a church that's really concerned about this issue and think that the church needs to be more proactive in dealing with it and we would like the church to be more inclusive of LGBT people, so we're pretty enthusiastic about it being changed," he said.

Two other Wellington churches, St Anselms Union Church and St Andrews on The Terrace, also did not support the assembly's ruling.