It followed this month's launch of the Action Plan for Healthy Waterways by the government.
That plan aimed to improve the ecological health of wetlands and streams via a range of measures.
These included setting higher standards of water quality in popular swimming spots, putting interim controls on land intensification, launching accelerated planning processes and other measures.
The announcement spurred strong complaints from some farmers that agricultural production could be made untenable in some regions.
But the NZIER report said this would not translate into overall economic harm for the nation.
"The likely impact on national GDP, due to the relatively small size of the dairy industry, is unlikely to be major at the national level," the report said.
"A reduction in GDP from (less) intensive dairy would, however, have uneven local effects, given the regional distribution of the sector."
The NZIER report then went on to say that more knowledge was needed to determine the real impact of the government's plan.
"The government has come to the view, which is well supported by scientific evidence, that water quality has deteriorated due to human activities," the report said.
"Its view is that the benefits of improving water quality are greater than the costs. However, we are not aware of any economic modelling that has been done at a national scale that confirms this presumption.
"The government should commission further, detailed and independent analysis of the effects of its proposals, outlining the benefits and costs at all levels."
But the report also said land users such as farmers did not always meet the costs of their own activities, and this was being addressed by the government's plan.
"What is being proposed is essentially that some of the costs of production that are currently not a financial charge to farms - water pollution and freshwater habitat loss or 'externalities' in the jargon of economics - will in the future be borne directly by farmers."
The report said if nothing else changed, it would imply that farm profitability must fall.
But things would change, due to creativity and innovation which has helped the farming industry in the past and could do so again.
It added a long lead time to bring in these reforms would also help.
- RNZ