Roxburgh farmer Glen McDonald only recently discovered "half the world's population" of the Teviot flathead galaxiid fish is living on his family farm.
The news came to light because of the Otago Regional Council's water quality plan changes.
The Director-general of Conservation has made a submission to the changes which suggests the inclusion of "areas with significant aquatic values" and restricts activities in zones 1 and 2 of those areas.
"The most significant habitats of acutely threatened indigenous freshwater fish should be protected from activities (such as waterway disturbance) that potentially may adversely affect them," the submission said.
Maps of those areas were included.
Mr McDonald has objected to the proposal and aired his views at yesterday's water plan hearing in Alexandra.
He said he was told about the galaxiids after asking the Department of Conservation why the family property at Lake Onslow, which he manages, had parts that were designated zone 1 and 2 areas of significant aquatic value.
"There's 300 of these fish in my creek which is apparently half the world's population, they said.
The last thing I want to do is harm the fish and I'm happy for them to be protected but my point is, this whole proposal by Doc is poorly conceived."
The fish appeared to be thriving under the current farming regime and there had been no consultation with the landowners before the area was included in zones 1 and 2 by Doc, he said.
"The stated aim of water plan change 6A is to maintain good water quality, not to maintain habitats for indigenous flora and fauna," Mr McDonald said.
The plan change should not be used to create "de facto" Doc reserves on private land without consultation, he said.
On Tuesday, panel member Clive Geddes said there had been a "large number of submissions" about the Doc submission, saying the issues raised were never intended to be addressed through the plan change.
He said the panel would have to consider whether it was appropriate for Doc to use the plan change in such a way.
The director-general's submission will be heard by the panel in Dunedin on October 9.
