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The Wellingtonia tree in Taieri Rd in Wakari was thought to be about 125 years old and expected to live for another 900 years.
The problem is that it is growing in the courtyard of a large house where people with intellectual disabilities live.
Owner of the house - Pact - wanted the tree removed because of the moisture problems it was causing, the leaf litter and the safety of residents if a large branch was to fall off.
During a resource consent hearing in April, Pact social housing manager Ferdi Koen said he could not understand why the house was extended to surround the tree in 1992.
The committee, made up of councillors David Benson-Pope, Andrew Noone and Lee Vandervis, sought a third arborist's opinion to clarify conflicting reports on the health of the tree.
''The committee was very reluctant to grant consent for removal of the tree, given its obvious significance.''
The committee decided there was a low risk of the tree or branches falling but the consequences for residents if it did happen were high.
Dunedin Amenities Society committee member Paul Pope said it was disappointing to lose a significant tree.
''There are situations where you have to be pragmatic. That tree is just too big. It is not designed for an 800sq m section and it is going to cause problems in the future.''