ACC said it respected the right of Greenpeace to protest peacefully.
However, Federated Farmers expressed its surprise at the protests, labelling Greenpeace "misguided".
The sector body's water spokesman, Chris Allen, said it was disappointing that the lobby group was opposing a scheme that has gone through a lengthy process and has stringent environmental conditions attached to it. "Greenpeace are demonstrating their anti-irrigation views and seem to oppose anything that gives New Zealand farmers climate resilience," he said.
Mr Allen said stored water gives communities the opportunity to develop good economic and environmental outcomes. He called the protest a "misguided publicity stunt".
"Greenpeace are barking up the wrong tree with dairy effluent - as those using the stored water will be doing so within strict resource consents and conditions that have been through a very rigorous process," he said.
Mr Allen said ACC had not been confirmed as an investor for the scheme and that out of 196 farms signed up so far, only one was a new dairy conversion. He said stored water gave communities the opportunity to develop good economic and environmental outcomes.
Politically, the protests have renewed Green Party calls for the Government to rule out any funding or investment in the "controversial" water storage scheme.
Hawke's Bay Regional Council chairman Fenton Wilson said many people had lost sight of the important connection between the Ruataniwha dam and the council's Tukituki Plan Change 6. However, Mr Wilson said the scheme and the plan change formed part of a wider programme to better manage water resources in the Tukituki Catchment and improve the Tukituki River.
He said the plan change had been developed to address the environmental issues in the catchment and that it would impose greater restrictions on existing farms in the catchment.
"When you view the Ruataniwha scheme through an environmental lens, it is part of a combined regulatory and infrastructure strategy designed to systematically improve the Tukituki River, related streams and wetlands," Mr Wilson said.
"That has always been the goal of the plan change together with the scheme."
The chairman said he was confident that together the plan change and the Ruataniwha scheme would provide a win-win situation for the region, improving the quality and quantity of water in the Tukituki River, giving farmers a secure water source for their farming operations and injecting more money into our local economy.
He said the reality was that without the Ruataniwha scheme, the Tukituki catchment would not receive the range of environmental benefits the scheme provided and the local Hawke's Bay economy would miss out on the major economic boost it so desperately needed.