Forest and Bird claims the Government is secretly planning open cast coal mines for the most significant conservation area in the Denniston Plateau.
The great spotted kiwi, fernbird, West Coast green gecko, and many rare insects and plants would be affected by the plans, according to the conservation group.
It said the unique landscapes of the plateau, in the Buller District, would be carved up and the best areas made available to new mining company Phoenix Coal.
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The plans were developed for the Ministers of Conservation, Energy and Resources, and Economic Development, according to Forest and Bird chief executive Kevin Hague.
They would set aside areas for coal mining and areas to be protected. Whareatea West, a conservation area on the plateau, would be set aside for open cast coal mining.
"This is public conservation land, and the most ecologically valuable area on the plateau; without Whareatea West the integrity of the whole plateau is lost," Hague said.
The spectacular Deep Creek would be protected from open cast mining but not necessarily from underground mining.
Minister for Economic Development Simon Bridges said ministers were still discussing the matter.
"It is a difficult issue as Buller Plateau has significant economic value but we also understand the need to balance that with the conservation values.
"Ministers will continue to discuss these matters and seek to better understand the trade-offs in order to find a suitable solution for all parties."