For the company, landscape architect Rachel de Lambert said chimneys were an evident feature of the site over the years. But they had come and gone.
Four chimneys bristled from the building when the concrete structure was built in 1946.
It was the sole survivor of that era.
A famous and original chimney from 1884 was knocked down in 1960 after being shortened for safety.
This also happened to the younger reinforced steel and concrete chimney. It lost 8m and its collar rim after painters found it was in a poor state.
Its topping in 2008 was followed by obsolescence: It was replaced by a shorter and slimmer all-steel flue for a now gas-powered boiler which provides the steam for the process of turning raw sugar into crystals.
Ms de Lambert said only 28.4m of the old chimney was left and its removal would not adversely affect the refinery's "style and character". There was still a boiler house chimney.
For the council, heritage architect Bryan Bennett said the refinery had a unique position in New Zealand industry and huge value to the region as a heritage landscape.
Loss of any of its collection of components, such as the chimney, would reduce that value.
He said NZ Sugar had insufficiently explored a wide range of ways to repair what was left of the chimney.
The company suggested its concrete chimney would cost up to $2 million to restore.