The fish and game council has raised concerns with the Otago Regional Council about issues in the upper Waipahi catchment and at Lake Tuakitoto.
Fish and Game Otago chief executive Niall Watson said they had yet to get an answer to their concerns that the rush swamp areas on the margins of Lake Tuakitoto were being developed into pasture.
"We want to stop any further development."
The area gave birds a place to nest and was an important habitat for protected species like fernbird, he said.
It was included in the schedule of protected wetlands in the regional council's Water Plan.
"This sort of thing cannot go on," Mr Watson said.
The council, which discussed the issue at its latest meeting, planned to write to the regional council to query the issue. The land was owned by the regional council, but leased out, he said.
"It was recognised as regionally important in the '80s as a wildlife habitat and recognised hunting area. It's one of Otago's major wetlands."
Fish and Game was also concerned about Cairn Swamp in the upper Waipahi catchment which it considered to have been "whittled away over time", Mr Watson said.
"Its drainage and destruction is not a desirable thing."
Fish and Game questioned the point of having a schedule in the water plan to protect these areas if that was not being done, Mr Watson said.
Otago Regional Council manager support services Gerard Collings said the council was aware of one instance at Lake Tuakitoto where a farmer, who had a grazing lease, regrassed an area. It was questioned whether or not it was wetland area.
As a result the council was considering reviewing the conditions of the grazing leases.
The council was also aware of another incident on Kuriwao Reserve land, but in that situation the council was bound by the perpetual leases the landowners held.
Regional council policy and resource planning director Fraser McRae said the council was consulting on a proposed change to the Water Plan provisions for wetlands.
The proposed changes included properly identifying all wetlands and their boundaries as well as altering the rule to ensure protection of all values, including the present key values.
"We want to make it clearer in what we are concerned about and make it easier for landowners to do what they need to do, provided they don't impact on those things."
