Federated Farmers say this is not a good, transparent process but underlines the need to work with government on the policy detail.
The federation's position remains that existing national regulations were sufficient, and required only minor amendment, not wholesale change.
"There is relief from farmers that the regulations may not be as bad as they could have been," Whanganui Federated Farmers president Mike Cranstone said.
"The setback of fencing has been reduced from an average of 5m to a minimum of 3m, the requirement to avoid any pugging has been modified so that it has to be managed and minimised," he said.
"The initial policy recommended the nitrogen limit be reduced from 6.9mg a lite to 1.0 mg, but this has been delayed for a year. This number seemed to be plucked out of somewhere, with no scientific evidence how this correlated to the health of aquatic life.
"This limit has been delayed for a year because scientists cannot reach a consensus. It is reassuring that now there is some science to back up the ideology, unfortunately there is still no economic impact analysis."
Cranstone said the vast majority of farmers support the goal of improving water quality, and they were proactively investing their own money to achieve it.
"It is great to see more funding being made available to support riparian fencing and planting," Cranstone said.
"The approach is still very prescriptive and wants to regulate across the country, hopefully the focus will move more to enabling the regional councils to target what will make the best environmental progress in each catchment.
"The Government looks to still have a bias against livestock farming, with horticulture and arable being exempted from 200kg/ha limits of nitrogen fertiliser being applied.
"Covid-19 has rammed home the importance that New Zealand has a diversified economy, the primary industries are contributing 70 per cent of New Zealand's export income and ministers in the government should not be picking winners. Monthly exports of meat topped $1 billion for the first time in March, despite the pandemic and a drought."
Cranstone said Federated Farmers commend the thousands of farmers who got involved in the consultation process, attending meetings and writing authentic and individual submissions on how the policy would impact their businesses and making constructive suggestions.
"We will need to stay engaged, because this policy just sets the intent, the regional council has the job of writing the regulations to achieve aspirational bottom lines. This process is estimated to cost the country's regional councils more than $1 billion, the government needs to consider how the implementation of its rules are being funded," Cranstone said.