The Ministry for Primary Industries (MPI) is rejecting criticism by Labour MP Kelvin Davis that its enforcement of laws for the export of swamp kauri is "slack".
Mr Davis says farmers are getting away with spraying, then draining, wetlands to kill off indigenous plants, so they can dig up the ancient timber.
He said the resource was being exported in raw forms.
But the ministry said it was not responsible for approving or monitoring the resource's removal.
It said in a statement that, in this instance, the Northland Regional Council was responsible for its regulation under the Resource Management Act.
"The Ministry for Primary Industries is responsible for administering the Forests Act 1949, which controls the milling and export of swamp kauri. MPI is not responsible for approving or monitoring the extraction of the resource or any associated environmental effects," it said in a statement.
"MPI continues to implement fully the quite specific legislative provisions that control exports. This includes inspecting all notified swamp kauri products for export to ensure they are permitted under the Forests Act and working with Customs to monitor export activities."
The Northland Regional Council did not respond to Te Manu Korihi's request for comment.
The ministry said the rules around what could and couldn't be exported had several layers to them, and that appeared to have lead to some public misunderstanding.
"Swamp kauri stumps and sawn timber from them can only be exported with MPI approval... Stumps can include the lower portion of the trunk, or stump logs, and this timber can be further sawn and manufactured in the export market," it said.
"Swamp kauri logs themselves can't be exported, only finished product made from them can. The act is very specific as to what constitutes finished product and includes finished components such as table tops."