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The investigation started after the Whatitiri Resource Management Unit (WRMU) filed a written complaint to NRC and the Department of Conservation (DoC), saying the works impacted on safe passage for fish and affecting their migration cycle.
The farmer said under a government scheme set up in the 1950s, a weir was built at that site to help supply water to farms in the area.
He has an easement for a water-take at the top of the falls and said he just repaired the weir as its concrete had been washed out over the years.
"We fixed the weir that provides landowners with water and did it in extreme drought. We already have easements to take water from there," he said.
NRC group manager regulatory services Colin Dall said a key requirement of the relevant rules was that the structure must provide effective fish passage under a wide range of flow conditions.
The works have reduced fish passage and this needs to be rectified, he said.
NRC is working with the DoC to determine what remedial action would be required to achieve effective fish passage.
Once options for remedial action have been determined, Dall said the people who undertook the works would be required to take appropriate remedial action to comply with the relevant fish passage rules.
"If this action is undertaken, the works would not require a resource consent under the Resource Management Act. The matter is still under investigation and at this stage it is not appropriate for the council to comment on the motives of the persons who undertook the works."
They will have to pay for any remedial work, he said.
At this stage, he said NRC has not made a decision on what formal enforcement action to take against those responsible.
There is a range of enforcement actions NRC can take, such as issuing abatement and/or infringement notices, enforcement orders and prosecution.
The maximum penalty for a successful prosecution is two years in prison or a fine not exceeding $300,000 for a person or a maximum fine of $600,000 for a company.
WRMU spokesman Millan Ruka said it was disappointing his hapū has not been consulted at any stage of the investigation thus far.