Avian botulism is thought to have killed around 80 birds in the Piako River in Waikato and more than 150 are displaying symptoms of the paralysing disease.
Gulls, black shags, grey teal, mallard ducks, grey ducks, pied stilts, white-faced herons and royal spoonbills are some of the species so far claimed by the disease.
Auckland Waikato Fish & Game has planned an operation to stem the outbreak near the river's outlet into the Firth of Thames.
The botulism is a form of food poisoning caused in water birds by hot weather releasing toxins from dead weeds or other pollutants in shallow, still water.
The toxin causes birds to lose control of their head and necks before the paralysis spreads to the rest of their bodies.