Conservation Minister Nick Smith has denied claims that a Department of Conservation (DoC) submission critical of the Ruataniwha Dam project was changed for political reasons.
A 32-page draft report set out the department's concerns about the way the Hawke's Bay Regional Council planned to manage water quality issues arising from the dam.
Dr Smith said he wasn't aware of the report until yesterday morning.
"But that's not at all surprising. This is a draft internal report of the department, of which ultimately senior managers did not agree with."
He said the department "took the view that they wanted to really focus in on the issues of about 22ha of DoC land that would be inundated by the dam rather than the fresh water quality issues".
In earlier reports he said he denied directing staff on the nature of their submission.
He said water quality issues were the primary responsibility of the regional council.
"They believe that this dam will enable water quality to be improved and minimum flows to be increased. That is an issue to be tested before the board of inquiry."
The dam project has two parts: Dam constriction for irrigation to farmers and Plan Change 6 - the improvement of water quality within the Tukituki catchment.
The unsubmitted draft report had been critical of its focus on phosphorous and failed to protect water quality causing harm to wildlife and could harm the Tukituki River estuary.
Green Party conservation spokeswoman Eugenie Sage said the department's advice on the project "has clearly been suppressed".
"The massive expansion of irrigation is one of this National Government's top priorities, so there are major questions to be answered as to why the department did not lodge its original submission," she said.
Ms Sage said the only other agency tasked with protecting the environment in the Hawke's Bay was the regional council, "but in this case, the council is the developer".
"DoC's role to advocate for nature is even more vital."
Hawke's Bay Regional Council chief executive Liz Lambert said it had a team of expert scientists on the project.
"The single nutrient management approach is relatively new in New Zealand and there is always a level of anxiety with something new," she said.
"While the Tukituki Plan Change 6 looks to manage phosphorus it also sets limits for nitrogen for the first time ever in this catchment.
"The conservative basis for nitrate limit setting to protect both native and introduced fish species present in the river is fully explained in the evidence of Dr Chris Hickey lodged with the Environmental Protection Authority and available on its website.
"The Ruataniwha Water Storage Scheme also offers the ability to create 'flushing flows' in the Tukituki River, which would wash out algae and slime." Ms Lambert said the council was taking a catchment by catchment approach.
"What works for the Tukituki Catchment may not be what works for other catchments."