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The Rt Rev Steven Benford sent an email to his congregation yesterday in response to the church’s national governing body passing Motion 29 on Wednesday, which allows priests to bless same-sex marriages and civil unions.
Priests are still unable to conduct same-sex marriages in the Anglican Church in New Zealand.
In his message, Dr Benford said he wanted to publicly affirm he did not want anyone to leave the church over the motion.
When contacted yesterday, he said the issue created a lot of debate within the Dunedin diocese.
It was a possibility members of the clergy and wider congregation would leave over the decision, he said.
"It has caused people to question whether their home was within the Anglican Church."
There were also people strongly for and against the motion who wanted to stay with the church, he said.
There was some confusion in the church about the motion, he said.
"People had come in saying ‘If the motion is passed, I will be compelled to conduct same-sex marriages’."
No-one would be compelled to, or even be able to, conduct same-sex marriages under the motion, he said.
No clergy members would be required to bless same sex marriages and none would be punished for refusing to do so, he said.
For those who did want to leave the church because of the issue, he wanted to make it as "easy as possible", he said.
"I think that someone who chooses to leave the church is still my brother or sister through Christ. I would want them to know that they were going with no ill feeling from me."
He did not want to publicly state his opinion on the issue.
When asked if he would personally bless a same-sex marriage he said he would "consider all applications".
"But I would not be telling the press what my answer would be, I’d be telling the couple".
The motion allowed people who had gone through civil unions or same sex marriages to have their partnerships formally recognised and endorsed by the church.
Dr Benford said he was concerned the issue would come to define the church.
"There is no perfect church and we are all sinners who are seeking to follow Jesus Christ in different ways and that’s what I put myself as as well."