Levels of facial eczema spores are high in some parts of the North Island.
Facial eczema can cause skin and liver damage in livestock, and in some cases can even kill them.
A monitoring programme by AsureQuality has shown extremely high spore counts in some areas, especially Waikato.
The agency says reporting from Gribbles Veterinary Pathology shows that clinical outbreaks have occured in some herds that have been treated for the disease.
Wanganui district manager Wayne Baxter says recent heavy rain in some regions would have helped to wash away spores in the pasture, but the levels will rise rapidly again.