Climate Change Minister James Shaw will advise against new mining permits though the government's position is to consider them on a case by case basis.
The Labour-led government is not ruling out new permits for coal mining, offshore oil drilling and fracking during a transition away from fossil fuels.
Prime Minister said there would be no mining on conservation land, but the government would consider other new permits "case by case". She said coal mining was not the country's future but there had to be a transition.
Mr Shaw said as Green Party leader he had always said the country should not be opening up any new fossil fuels.
"As Minister for Climate Change I have to say that in the future, if you're going to get to a zero carbon economy, there will be a point at which it's simply incongruous to be issuing those [new mining permits].
"I would advise against it, as Climate Change Minister."
While fossil fuels were not the country's future, exploration industries had to have a transition period, he said.
But to meet the government's promise of a carbon neutral New Zealand by 2050 there would be a point at which no new permits for exploration would be issued.
"You simply cannot get to net zero [carbon emissions by 2050] and do that."
Mr Shaw declined to say whether the government would allow a proposed open cast mine, Te Kuha, on the West Coast.
He said the mine project was very far advanced under the previous government and there were constraints on ministerial powers.
The mine has won resource consent and needs permission from the Conservation Minister for access across conservation land.
Mr Shaw said for future decisions, the government would consider legislating so environmental considerations can be taken into account, he said.
NZ needs rapid transition from fossil fuels - Greenpeace
Greenpeace executive director Russel Norman says no new mining permits should be issued if the government is serious about climate change.
"If we're going to avoid catastrophic climate change we can't afford to burn the existing known fossil fuel reserves - we can't even afford to burn half of them - at a global level," he told Morning Report.
"We need a rapid transition away from fossil fuel."
"A transition means reducing the use of fossil fuels, it doesn't mean looking for new fossil fuels as the Prime Minister seems to be leaving the door open to.
"If we're serious about climate change we simply can't be taking a case-by-case approach to oil gas and coal.
"We need to have a black and white position which is no new permits."
He backed a transition period for affected workers but said the first step was to stop issuing new permits.
The organisation representing oil and gas exploration firms supports the Prime Minister's stance.
Petroleum Exploration and Production Association of New Zealand chief executive Cameron Madgwick backed Ms Ardern's view that a transition was necessary.
Mr Madgwick said gas may be used for preference over coal in the next few decades.
"Not all fossil fuels have the same emissions. Coal has almost twice the emissions of gas. So we would expect there will be some choices made as to which of those fossil fuels are burnt over the coming decades.
audio] http://www.radionz.co.nz/national/programmes/morningreport/audio/2018626906/oil-gas-industry-supportive-of-pm-s-position-on-fossil-fuels "Oil has more emissions than gas but depending on the application can also be lower than coal" - Cameron Madgwick
"As a result it's likely that more gas will be burnt and that will of course have have an overall better impact on overall emissions."
The government's plan for net-zero emissions also involved offsetting emissions by planting of trees and better energy efficiency, he said.
If somebody was going to make the choice between a new gas development and a new coal development we'd certainly be pro-gas. But you have to talk to the coal industry about whether coal mines are important or not."
The government yesterday unveiled the first steps in its plan to reduce carbon emissions.
It will set up an interim committee to help it draft legislation to put the carbon neutral promise into law and establish an independent Climate Change Commission.
Public consultation is planned before the Zero Carbon Bill is introduced by the end of October.