The DCC has flown the tino rangatiratanga every Waitangi Day since 2008, and consults with local runanga before flying the Maori sovereignty flag on the civic centre building.
DCC communications and marketing manager Graham McKerracher said to his knowledge the flag had never been an issue in Dunedin, but ''in some places may be controversial''.
The Queenstown Lakes District Council, Clutha District Council, Gore District Council and Southern District Council would not fly the flag as the possibility of doing so had never been raised.
The Otago Regional Council and Invercargill City Council would not fly the flag due to their offices being closed.
A spokesman for Waitaki District Council said flags were flown ''under instruction'' from the Department of Internal Affairs and there was no plan to fly the tino rangatiratanga.
Environment Southland never flies flags, except on occasions when Internal Affairs requests the New Zealand flag should be flown at half-mast.
The Central Otago District Council was not in a position to comment on the flag yesterday.
Otakou kaumatua Edward Ellison said he received a call from Dunedin Mayor Dave Cull about flying the flag, and, ''we had no issues with it''.
''We have a closer working relationship with the DCC than the other councils, but over time, as we develop those other relationships these sorts of things might come to pass.
''We think it is good and an appropriate thing to do on Waitangi Day.''
The Ngai Tahu Treaty Festival will be held at Onuku Marae, in Akaroa, this year.
The annual event is shared between the three locations where Ngai Tahu signed the Treaty of Waitangi: Te Rau Aroha Marae, at Awarua (Bluff), Otakou Marae and at Onuku Marae, Banks Peninsula.
