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The 98-year-old cathedral in the Octagon was at the heart of a "troubled and troubling diocese", St Paul’s Cathedral Dean the Very Rev Dr Trevor James said.
In an impassioned blog post to parishioners, he said members of the Cathedral Greater Chapter had met the Diocesan Council to discuss the plan to reduce the number of Anglican parishes in Dunedin (including the cathedral) to four.
"A question is whether to keep the cathedral or not and the debate disclosed uncertainty as to why we should have a cathedral and the value [or not] that it represented," he wrote.
The diocese was "absolutely not" considering selling the cathedral. However, it was important its future was considered on an equal level to other parishes at risk, he said.
At present, there are seven Anglican parishes in Dunedin.The uncertain future of the cathedral was symbolic of a larger crisis facing the Anglican church in the city.
"The problem is the diocese. The diocese is broke and we’ve got Lord knows how many churches in Dunedin and a population that is not growing."
People had a "complete lack of trust" in churches and the church was fighting a growing "crisis of faith".
This struggle was exemplified last year when the church asked parishioners to give the cost of a cup of coffee each week so a bishop could be retained in the city.
The church was yet to find a replacement for the Bishop, the Rt Rev Dr Kelvin Wright, who would retire at Easter.
"The diocese is at the point where they have to make some hard decisions ...
"If they want to get it done by 2020, they will have to make some hard decisions fast."
Three representatives from the cathedral would meet three members of the Diocesan Council to discuss the situation.
Anglican Church spokesman Jayson Rhodes said the decision on the future of the cathedral lay with Dr Wright.
"The bishop has advised the national church the option to sell is not even on the table."