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Federated Farmers says the "vast majority" of dairy farmers act responsibly on environmental matters.
An Otago Regional Council report on dairy-farm inspections released this week showed the council would be taking 21 prosecutions involving 18 of the region's 379 dairy farms.
Federated Farmers Otago dairy chairman David Wilson said they did not defend wilful polluters, but the majority of farmers (75.5%) were doing a good job.
"Only 5% are being prosecuted, a drop in serious non-compliance when compared to last year."
It was also important to note farm numbers had increased by 7%.
While 71 farms (18.7%) were judged to be in minor non-compliance, up on last year, minor non-compliance was usually easy to rectify, he said.
Federated Farmers was working with the council to correct the poorest-performing farmers and it would be nice to acknowledge this as working, Mr Wilson said.
There were concerns about the "seemingly low" number of re-inspections as the federation knew from other regional councils that most farms deemed to be in minor non-compliance became fully compliant upon re-inspection.
Federated Farmers wanted the same level of prominence given to urban effects on the environment as to those of farming.