Conservation Minister Eugenie Sage says the opening of two vast new areas for prospecting was unfortunately timed, given moves to halt new mining on protected land.
Environmentalists are also demanding to know why officials have just lifted a three-year moratorium on the South Island areas - one in Otago covering more than 33,000sq km and another in Nelson covering nearly 8000sq km.
Both had been closed to prospecting while regional aeromagnetic surveys were undertaken, and to allow an allocation strategy for the areas to be developed.
While applications for other types of minerals permits continued to be accepted over the closure period in the two areas - and some permits were already in place there - New Zealand Petroleum and Minerals (NZPM) lifted the moratorium on July 8.
The land that was under the prospecting moratorium includes conservation land, including reserves, conservation areas and national parks.
It included parts of Mt Richmond Forest Park, Victoria Forest Park, and numerous other rich biodiverse areas classified as stewardship land.
"Dun Mountain and the Red Hills are a stunning, special part of Mt Richmond Forest Park," Forest & Bird chief executive Kevin Hague said.
"The unusual geology creates a rich red in the rocks, and very specialised habitats for plants like giant forget-me-nots, geraniums, as well as stunted southern rata.
"Over a dozen threatened species flourish in this seemingly stark landscape and thousands of visitors enjoy the diversity as they walk this section of national Te Araroa Trail.
"This is not an area that should ever be opened to mining."
The areas also included parts of both Kahurangi and Nelson Lakes national parks.
Hague said these should be immediately excluded as they were protected from mining - something that had been vigorously fought for.
The Otago areas include the Rock and Pillar Conservation Area, as well as numerous other pieces of stewardship land which were previously pastoral leases, where the public has paid to protect the land.
The Piata Scenic Reserve was recently purchased by the Department of Conservation to protect bog pine.
Forest & Bird has questioned why this was allowed to happen when the Government was just months away from beginning consultation on how to fulfil its pledge of protecting all public conservation land from mining.
"It beggars belief to deliberately undo the closure just before consultation is planned on how to protect these areas from mining," Hague said.
"Having 40,000 people march down Queen St in 2010 made it pretty clear that the public does not want mining on conservation land.
"To even stand a chance of protecting our unique plants and animals we need our publicly-owned conservation land to be used for conservation, not digging huge holes in the ground."
Sage acknowledged the timing of the moratorium ending was unfortunate, given the work being done on the "no new mines on conservation land" policy.
"However, as ministers have said previously the status quo applies until the law changes, through finalising and implementing the no new mines policy," she said.
She noted that having a prospecting permit from MBIE did not guarantee that DoC would grant access to conservation land.
Before DoC or ministers allowed access to conservation land for prospecting, exploration or any mining activity, they reviewed the impacts the activity was likely to have on conservation values, such as unique ecosystems and wildlife.
Low impact prospecting had been permitted on conservation land in the past.
While mining is prohibited on Schedule 4 land, minimum impact activities such as geological, geochemical and geophysical surveying are permitted under the Crown Minerals Act.
Taking samples by hand or hand-held methods is also permitted.
An MBIE spokesperson said operators seeking minerals permits would also need to comply with the Resource Management Act, under which regional councils were responsible for managing environmental impacts.
It was possible for a minerals permits to be approved, but a resource consent to be declined, the spokesperson said.
"It is important to note that the granting of a permit does not give the permit-holder an automatic right to access the land – access to the land, generally for exploration and mining activities, needs to be arranged with the landowner and occupier."
The Government planned to release a discussion document around its proposed policy of no new mines on conservation land within the next three months.
No existing mining permits were expected to be affected and the consultation only related to new mining on conservation land.
In New Zealand, most mining, and all large scale mining employing more than 100 people, occurred away from these protected areas.