However, she had found no evidence that timber was being exported illegally. Photos purporting to show swamp kauri logs overseas had been taken in New Zealand, she said.
She agreed, however, that the system used until a few months ago for verifying the source of swamp kauri was not effective.
Milling statements, which were supposed to prove logs had been extracted legally, were issued on a "high-trust system," with minimal inspections before or after extraction.
The MPI believed protecting the environment was the regional council's job, but because extraction of swamp kauri from non-indigenous sites was a permitted activity, no council approval was needed. That meant extraction was carried out with little central or local government oversight, "creating a possibility that milling statements had been approved based on inaccurate, incorrect or false information".
Ms Provost said new rules brought in by the MPI in July would reduce that risk. Now operators had to inform the council any time they wanted to extract swamp kauri, and the ministry would try to visit every site as part of its new milling statement approval process.
It was also planning to produce a new guide outlining what it considered a finished product, and had agreed to increase staffing in Whangarei to improve inspections of sawmills and export shipments, Ms Provost saying that better and more readily available information about swamp kauri would help alleviate public concern.
Northland Environmental Protection Society chairwoman Fiona Furrell said her only disappointment with Ms Provost's response was that she had taken the MPI's word that the swamp kauri log photos had been taken in New Zealand. Group members had been to swamp kauri factories in the US, and verified that some photos had been taken there. In one video clip port workers could be heard speaking Italian as they unloaded swamp kauri.
She agreed with Ms Provost that the definition of finished product would have to be tested in court. The society was planning legal action to do exactly that, she said.
Meanwhile Green MP Eugenie Sage said Minister for Primary Industries Nathan Guy had been wrong to ever assert that everything was "fine and dandy" with the mining and export of ancient swamp kauri, given the Auditor-General's finding that the ministry's regulation of milling and exports had shortcomings.
"The further changes that the Auditor-General suggests for the ministry and councils to now make highlight on-going shortcomings in the control of the mining, milling and export of ancient swamp kauri," Ms Sage said.
"The government's new management measures announced in mid-July are failing to prevent Northland's wetlands from being plundered, or to protect the cultural taonga that ancient swamp kauri represent.
"The gaps in the government's regulatory oversight identified by the Auditor-General also suggest that the ministry and councils previously may have allowed substantial milling of ancient kauri from areas of indigenous wetland.
"At the time that the Minister was claiming that there was nothing wrong with the regulation of swamp kauri, there was no reliable system in place to ensure that the ancient swamp kauri being milled was being mined in line with the law."