Hundreds of kanuka trees were cut down recently at the North Taieri property and the Dunedin City Council confirmed it was investigating after receiving a complaint.
University of Otago botanist Prof Janice Lord said destroying that much native forest was "supremely arrogant" and the area was irreparably damaged.
In a statement, the owners, who requested anonymity, said they contacted the council before cutting down the trees and believed they took the correct steps before starting the work.
"We have lived here for many years and care for our land."
The kanuka was overgrown and had become a fire hazard, which prevented the owners from effective year-round solar energy, a necessity for their off-the-grid home.
They would not comment further on their actions because of the possibility of enforcement action and litigation.
"Suffice to say we deny any suggestion of wrongdoing."
Prof Lord, who contacted the Otago Daily Times about the issue, said native forests were valuable to local wildlife, as they housed birdlife, fungi and produced seeds.
People might see it as only a small piece of forest, but it was another example of native forests being destroyed through "death by 1000 cuts".
Those who owned land with native forests had a responsibility to look after them, she said.
"It doesn’t belong to you.
"This forest is more important than you are as an individual."
While some of the kanuka was younger, other pieces seemed to show 100-200 years of growth, she said.
The trees had also been cut down near the Silverstream, which meant soil would be washed down straight into the water, she said.
The area was prone to flooding, which Prof Lord said would be made worse by the clearing.
The owners said the affected land was "considerably higher" than Silverstream and the risk of flooding was expected to remain low.
