It comes after it was confirmed more than 1000 waterfowl died near the Waikouaiti wastewater treatment plant in Otago after being infected with the disease.
DOC senior biodiversity ranger Ian Fraser said botulism looks to have caused the bird deaths at the Waitarakao Washdyke Lagoon, near Timaru.
Tests will be done to rule out any exotic disease.
Avian botulism is a naturally occurring bird disease triggered by environmental conditions which prompt a bacteria, found naturally in soil, to produce a toxin that causes birds to die.
Outbreaks are localised and clear naturally when conditions change.
DOC said it is monitoring the situation and plans to collect and dispose of some of the carcasses to reduce the spread to other birds in the area.
