"Parishes within those dioceses are threatening to leave if it goes through, so they are trying to find a way to hold it together," she said.
Two parish priests, in Henderson and Hamilton West, walked out of the Church with part of their congregations two years ago when the last General Synod at Waitangi voted to set up the working party on blessing same-sex marriages.
Dr Jacobi said both parishes still had functioning Anglican churches even though their numbers were depleted.
"When people leave, they can't take the buildings with them," she said.
This time she said several more parishes would quit if same-sex unions were blessed.
"We are all feeling a bit despondent at the moment, but we will wait and see what the outcome is," she said.
However, Church spokesman Rev Jayson Rhodes said the bishops and dioceses of Christchurch, Wellington and Nelson were all committed to finding a way to keep the Church together.
"There has been no threat of any walkout at any point," he said.
"All the people here are wanting to see progress. What the shape of that progress is, is still being determined. Everybody listened to everyone yesterday and said we'll need some more time for consultation to see what mechanism can hold us together and bring some progress."
The working party, chaired by Auckland lawyer Bruce Gray QC, argued that Church doctrine had always been "dynamic", citing examples such as abandoning a ban on remarriage of divorced people and dropping the bride's marriage vow to obey her husband.
It argued that same-sex relationships could be blessed because they expressed fundamental virtues of marriage such as "self-giving love", physical union and life-long faithfulness.
"What is being proposed is the blessing of a relationship that manifests a number of virtues that honour each partner and God (and thus can be called a 'Holy Union')," the report said.
"The marriage itself will have occurred elsewhere, and the working group acknowledges that this will fall short of some Christian same-sex couples' hopes because they cannot be married 'in church'."