The council revealed it was behind the removal of the Max Smith tree, a 45-year-old liquidambar planted on private land owned by the Maerewhenua Corporation.
It was a mystery that stumped spokesman Errol Wills, who initially described the incident as "the rural equivalent of a ram-raid".
The tree was named after the project engineer of the Upper Waitaki hydro-electric power scheme in the 1970s.
When the Otago Daily Times asked the council if it had taken the tree last week, it said it had checked with its contractors and none were aware of it.
However, the truth was revealed following further investigation by the council.
It posted to social media to say it had done "some deeper digging" and discovered its contractors had removed the tree.
When water services staff went out to sample effluent from the town’s treatment system, they found a limb from the tree had fallen and covered access to the septic tank.
A contractor was instructed to remove the fallen limb that was impeding access to the septic tank, which was preventing the sampling needed to comply with resource consent requirements.
When the contractor visited the site, they found the tree was half uprooted and made an on-site decision to remove the tree entirely on safety grounds.
Chief executive Alex Parmley said "we sincerely apologise for this and for not unravelling who was responsible sooner."
The council would plant a replacement memorial tree in honour of Mr Smith in consultation with the Duntroon community.
It would also contact the landowner and apologise.
Mr Wills said he suspected the council might have been the culprit, but did not want to point fingers.
The council often spoke about consultation with the community, but it had come on to the property and taken the tree without consent.
It was disappointing the council had not followed its own values, he said.
