The department gave written consent for NZSki's project to extend a leaners' slope at the Remarkables skifield.
However, an internal Doc report by ecology technical adviser Brian Rance had concerns about the proposal in terms of the cumulative effects on the area's ecological values.
It suggested a range of mitigation and compensation measures be introduced beyond what the applicant suggested.
These did not appear in the land-use conditions.
Aside from what NZSki said in its application, the consent only required the applicant not to import soil to the site and consult a qualified herpetologist in the event lizards were found.
The ecological values were of significance and the impact on ecological values was high, he said.
Forest and Bird Otago and Southland central regional manager Sue Maturin said it was "pretty disappointed" the department was "complicit" in the wetland's destruction.
"The wetland is small but it is significant. There's quite a high diversity of indigenous species.
"It's the constant nibbling away of seemingly small but significant areas of biodiversity which is contributing to an alarming number of threatened species."
She was tired of companies and organisations "finding their way around policies trying to save our remaining national treasures".
In the future it wanted to be assured any application to destroy wetlands was publicly notified, she said.
The project required further consent from the Queenstown Lakes District Council and permission from the Otago Fish and Game Council, and iwi representatives.
Doc southern South Island operations director Aaron Fleming said a detailed assessment of the land and application was undertaken by Doc and an independent monitor with more than ten years' experience in the area.
"[They] ... concluded that the impacts of the work could be minimised with appropriate mitigation."
While they were considered regionally significant wetlands, this criteria did not on its own determine the outcome of an application, he said.
Doc and NZSki had an existing protocol to manage environmental rehabilitation during and following works at the skifield, he said.
