Fish and Game Otago has appealed the Otago Regional Council's proposed plan change 2 (regionally significant wetlands) to the Environment Court on four grounds - the removal of indigenous water fowl from the list of values, the "wetland inventory" having no legal status, and it allowed existing drains to be used to fix water pooling outside a wetland.
Environmental officer Peter Wilson said the most concerning issue was that the plan also removed the automatic consideration Fish and Game had as an affected party.
It meant Fish and Game did not get to have a say on consents which were not publicly notified involving activities in lakes, rivers and regionally significant wetlands.
Other "affected parties", such as the Department of Conservation and Ngai Tahu, were in a similar situation, he said. There were already cases of which the council had not been informed.
Chief executive Niall Watson said being excluded had the potential to affect species the organisation was responsible for managing.
Fish and Game took the regional council to court about 10 years ago over its attempt to remove introduced game birds as a value from wetlands and it was resolved in mediation, so there was a "precedent", he said.
The plan was also being appealed by TrustPower and Meridian Energy and mediation would be the next step.
If that failed, it would go to court but that was unlikely to happen until next year, Mr Watson said.
