Officials are standing by their definition of wetlands which is under fire from many sides.
Industry and conservationists say the changes that kicked in last month were last-minute and not consulted on, and independent commissioners hearing a mining application have criticised them as ambiguous.
Ministry for the Environment (MFE) admitted it was a late change.
"The definition was changed between the draft and the final [National Policy Statement (NPS) for Freshwater Management], as a result of consideration of submissions and further conversations," the ministry said in a statement.
It held two years of talks across the sector and received more than 17,500 submissions on the whole NPS.
"MFE stands by the definition of natural wetlands," it said.
"However, we will continue to listen to the views of business and regional councils as we work to implement the regulations make sure the implementation of the policy is practical and effective."
The definition adopts the Resource Management Act's definition of "permanently or intermittently wet areas, shallow water, and land water margins that support a natural ecosystem of plants and animals that are adapted to wet conditions".
But the NPS definition then excludes areas of improved pasture, artificial and geothermal wetlands.
"As the regulations are implemented, different views will surface, as has happened with the quarrying industry, and we will work through the issues raised," the ministry said.
Quarry Association members have written to the government protesting that the wetland rules will lock up millions of tonnes of rock or shut them down.
It is the wording around improved pasture that has generated most confusion.
"An improved pasture means an area of land where exotic pasture species have been deliberately sown or maintained for the purpose of pasture production, and species composition and growth has been modified and is being managed for livestock grazing," the ministry said.
However, Forest and Bird said the reference to an area "dominated by (i.e. more than 50 percent of) exotic pasture species" was vague, wide open to litigation over its interpretation, and should be changed
The quarry industry is also upset at a blanket ban on modifying any natural wetland.
The NPS definition of natural wetland now also applies to the National Environmental Standards for Freshwater, which prohibits a natural wetland being drained.