An environment group has gone to court over claims a Canterbury farmer wiped out nearly a third of the national population of a rare and threatened plant.

Forest & Bird says the vast majority of shrubby tororaro is found on one farm on Kaitorete Spit, a narrow stretch of land between Lake Ellesmere and the sea, and claim the farm's new owner sprayed and cultivated three of the farm's eight paddocks.

The group alleged the clearance and sowing of oats damaged or destroyed an estimated 29.3 per cent of the total nationwide wild population - and may have also affected numerous other threatened species that live on the site, including birds, lizards, plants and invertebrates.

The farmer, Brent Thomas, told RNZ he was "horrified to find ourselves in this situation" and was working to reach a collaborative solution.

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The Department of Conservation was meanwhile seeking to buy some land from Thomas to be turned into a reserve, which would protect some of the remaining plants.

Forest & Bird chief executive Kevin Hague said biodiversity was "in crisis" in New Zealand.

"Often it's a case of small impacts adding up to a major loss, but here a single incident has made it far more likely for a species to go extinct in the wild," he said.

"That these plants remain in people's gardens does nothing to mitigate the impact – we have a responsibility to not let these species go extinct in the wild. We don't want to see our threatened plants and animals only remaining in zoos and people's gardens."

The group has applied the Environment Court to prevent further activity at the area; much of the rest of the national population of the plant existed on the farm's other paddocks, the group said.

Forest & Bird was also concerned about a Christchurch District Plan rule that allowed clearance of indigenous vegetation in "improved pasture".

It was believed the clearance was carried out under this rule, which was considered at District Plan hearings in 2016.

"We don't have a problem with a well-crafted rule that allows normal farming activities while protecting important native species," Hague said.

"In this case, the rule is poorly drafted and lacks clarity."

The group has sought declarations regarding the improved pasture rule and definition, including that the rule is so uncertain that it could be unenforceable.