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.