In response, Environment Southland (ES) councillor Robert Guyton said the council was "taking heed" of the report and farmers had been trialling methods to reduce emissions and at the same time improve soil and animal health.
ES policy, planning and regulatory services general manager Vin Smith reiterated that message and said ES had no jurisdiction over greenhouse gas emissions and were not able to consider emissions as part of any consent application.
"While we consider cow numbers as part of a dairy consent application, we do so for environmental impacts, particularly for water quality. We know dairy farming can have a significant impact on water quality, however these impacts can be limited when done well".
Southland Federated Farmers President Geoffrey Young said while agriculture did contribute a comparatively high level of emissions, the majority were methane, "which is a short-lived gas, and while stable in quantity does not contribute to global warming".
Despite that, changes were happening and sustainability was being improved.
"The number of animals on farms is reducing, while production increases, because Southland farmers are outstanding food producers, and are getting better at it every day".
In the 2016-17 season, DairyNZ's website said there were 563,017 milking cows in the region.
For the 2017-18 season, there were 583,240 milking cows and for the 2018-19 season, 591,987.
DairyNZ strategy and investment leader Dr David Burger said it was committed to farming within environmental limits and did not support growth or intensification where this would exceed agreed limits.
"Cow numbers are stable now and the dairy sector, and our 12,000 farmers, are committed to taking responsibility for the care of our people, animals and our environment".
A DairyNZ spokeswoman also wanted to clarify it was not only cows contributing to the agricultural emissions; Southland's 4 million sheep emitted only 10 per cent less methane and nitrous oxide than cows.