The power company has been considering options for hydro schemes on the river and was one of the groups which opposed an amendment to the existing Water Conservation Order (WCO).
A special tribunal, appointed by the Ministry for the Environment, last month recommended the WCO be amended to prohibit dams.
The tribunal said the change was necessary to protect the habitat of a small native fish named Gollum galaxiid - a unique species, found only in the Nevis.
Pioneer chief executive, Peter Dowling, said although the company appreciated the tribunal's concerns, it did not believe amending the WCO was necessary for the galaxiid's protection.
"From the evidence presented at the hearing it appears to us that the greatest threat to the galaxiids is the existing trout which prey on them.
Amending the order as recommended will not remove this existing threat to the galaxiids," he said.
The remedy proposed to protect the native fish seemed "overly conservative".
Pioneer wanted to keep the option open for dams on the river and said if any future hydro scheme was proposed, resource consent would be required.
The New Zealand and Otago Fish and Game Councils proposed the amendment to the WCO.
Otago Fish and Game chief executive Niall Watson said last night the organisation was disappointed Pioneer "can't accept that the natural, amenity and heritage values in the Nevis Valley make power development there wholly inappropriate".
The Environment Court will now hold an inquiry and provide a report and recommendations on the matter to the Minister for the Environment, Nick Smith.
