Dr Smith said the department ``took the view that they wanted to really focus in on the issues of about 22 hectares of DOC land that would be inundated by the dam rather than the fresh water quality issues''.
Dr Smith 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.''
But 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.''
Ms Sage said the only other agency tasked with protecting the environment in the Hawkes 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.''
She said the Ruataniwha project could be used a model for future developments and the regional council's planning regime for water quality could be copied elsewhere.
The $256 million scheme involves the construction of an 83m dam on the Makaroro River in Central Hawke's Bay, creating a reservoir capable of storing 91 million cubic metres of water which could potentially irrigate 20,000-30,000ha, depending on land use.
The board of inquiry considering the project begins hearings next month and is expected to issue its decision next April.
