Fonterra says more than a quarter of dairy farmers supplying it with milk need to improve their effluent management.
The cooperative has completed its first-ever annual health check of 10,500 suppliers.
It began checking effluent systems on farms last August, to improve compliance with local authorities' dairy effluent rules.
Fonterra's supplier and external relations director, Kelvin Wickham, says the majority of farms are complying with effluent rules.
But he says there are issues with 2800 farms and these have been referred to Fonterra's sustainable dairying advisor team, to come up with a plan for fixing their effluent problems.