About 300 dead birds have been discovered around the Bromley oxidation ponds.
Initial indications suggest the birds have fallen victim to avian botulism, a disease which causes paralysis in birds and often results in death.
Eliminating avian botulism is difficult because the toxin producing bacteria occurs naturally in the environment.
Outbreaks of avian botulism are not uncommon in New Zealand and other parts of the world and have occurred in Christchurch previously.
The Council is removing the dead birds in an attempt to slow the spread of the disease.
It is also checking other wetland areas to check whether any of them have been affected by the disease, which is caused when birds eat toxin produced by clostridium botulinum bacteria.
Clostridium botulinum naturally occurs in soils found in ponds and wetlands. It is harmless until the right environmental factors occur.
Most avian botulism outbreaks are caused by ducks eating maggots that have fed off dead birds, which is why the Council is trying to remove any dead birds as quickly as possible.
The majority of the birds that have been found dead around the oxidation ponds are paradise shelducks although some mallard ducks have also fallen victim to the disease.
Avian botulism cannot be transferred to humans but people are advised not to handle any dead birds with their bare hands.