Devon Dairy Farm had cleared 12.2ha of indigenous vegetation to use as pasture land for intensive dairy grazing, he said.
This action was contrary to the Queenstown Lake District Council's District Plan and required a resource consent - which the company did not have.
Judge Dwyer said it was "practicably impossible to reinstate the area in its original conditions''.
Judge Dwyer said it was the first appearance of the defendant in court, but the offence was serious.
Defence counsel Michael Walker said the company was "extremely remorseful'' and to mitigate the actions, it engaged an ecologist who identified another area of 34ha in the farm - which contained 27 different species of indigenous plants.
It subsequently made an legal agreement with QEII National Trust for the registration of a covenant over the land, providing permanent protection for the area.
Walker said the company was "an extremely positive example of modern day dairy farming'' and had a track record of community involvement, including an agreement with the QLDC to provide access through its property for a new sewage pipe.
This would mean that ratepayers would save about $6 million, he said.
Judge Dwyer fined Devon Dairy Farms $42,000 and ordered the company to reimburse the Queenstown Lakes District Council $23,039 and pay court costs.