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A table published by the Taxpayers Union shows, of the eight Otago and Southland local councils, ratepayers in the Southland District Council area had the cheapest average residential rates of $1669.
Those in the Queenstown Lakes District Council area paid the highest with an average of $2476.
Dunedin ratepayers have the 54th highest average residential rates in the country out of 66 districts, with an average of $1994, the cheapest of all the metropolitan councils.
Western Bay of Plenty ratepayers pay the highest average residential rates in New Zealand at an average of $3192 per ratepayer while in the Mackenzie district they pay the lowest, at an average $1593.
Dunedin Mayor and Local Government New Zealand president Dave Cull said it was unfair to compare different councils as they each provided different services and served different communities.
There was a genuine rates affordability issue across New Zealand but there was no alternative funding base for councils, Mr Cull said.
"Our reliance on the narrow funding base which rates provide is not sustainable and we know while costs keep rising for councils' ratepayers, incomes aren't keeping up."
Also included in the Taxpayers Union's table was the number of employees each council had.
The Dunedin City Council had 1371 employees the third highest, although figures from the Christchurch City Council were not included.
That is more than the similarly sized Hamilton City Council with 977 employees and Tauranga City Council with 795.
But Mr Cull said that figure also included the council-owned companies and again did not provide the full picture.
"I believe those two councils use contractors a lot more for their services than we do in Dunedin so while when compared against each other it may seem Dunedin employs more people, those same services are being provided and paid for, just in a different way," he said.
Taxpayers' Union executive director Jordan Williams said Mr Cull was clear what part of the figures and comparisons he objected to.
The point of the table was to allow people to easily compare their local council's performance and financial position against similarly sized councils and types, he said.