The three charges were "unavoidable", following a year-long investigation by the Waitaki District Council, a council spokesman said.
The council started investigating after it became aware in September last year that the vegetation on the farm in the Ramrock Rd area had been cleared, he said.
The area cleared without consent measured about 462ha.
It was home to grand and Otago skinks.
Both species, which grow as long as 30cm, are unique to Otago and are some of New Zealand’s rarest reptiles.
The charges are for breaches of section 9 (3) of the Resource Management Act 1991, by carrying out land use activities in contravention of the council’s district plan.
A prosecution had been "unavoidable" given the size of the area cleared, the council spokesman said.
The district plan states no indigenous vegetation clearance is allowed in an area of skink habitat, except for the purpose of infrastructure maintenance.
Council chief executive Alex Parmley said the rules under the Act were to protect indigenous biodiversity and the council had a legal duty to uphold them.
Some of the rules prevented what were seen as traditional farming practices, and the council would work with the farming community to help people understand them.
"Prosecution of anyone in our district is a last resort and something we take no pleasure in and wish to avoid if possible.
"In this case, the amount of area cleared is so large, a prosecution was unavoidable."
The council urged any property owners and contractors contemplating clearing areas of indigenous vegetation to contact it and discuss district plan rules first.
Stoneburn Station owner Alasdair Lindsay confirmed this week Stoneburn Station Ltd had been charged.
He declined to comment further.
Forest & Bird Otago Southland regional conservation manager Chelsea McGaw said it was pleased with the council’s decision.
The consequences of the clearance were even greater than the endangerment of native reptiles.
There was a perception tussock was less valuable than other vegetation, which was not the case, she said.
Not only was it a biodiversity hotspot for lizards and invertebrates, it was good at sequestrating carbon and purifying water.
Almost all of Dunedin’s drinking water came from tussock land.
Unfortunately, the damage at Ramrock Rd had already been done.
"I hope its a deterrent to people in the future, that they will stop doing this kind of thing so we can stop even more loss," she said.
Forest & Bird received an anonymous handwritten note in April alerting it to the clearance and the council’s investigation.
The note also suggested the council’s investigation had been delayed, potentially due to "internal interference", Ms McGaw said.
A council spokesman said the council categorically denied any interference.
The investigation was a slow and detailed process rather than delayed, he said. — Additional reporting Hamish MacLean
