Canterbury District Health Board says whitebait should not be taken from the Avon and Heathcote rivers in Christchurch due to the risk of contamination.
The whitebait season began on Wednesday in all but the West Coast and the Chatham Islands.
Medical officer of health Dr Alistair Humphrey says the Avon and Heathcote rivers were polluted by sewage following the earthquakes.
He says whitebait caught in those rivers are likely to be contaminated by the parasite Giardia, which can cause diarrhoea that can last for months.
Dr Humphrey says the parasite eggs are not killed by freezing.
Meanwhile, the Department of Conservation says whitebaiting in some Otago rivers could be dangerous today due to heavy rain.