Bay of Plenty chief medical officer of health Phil Shoemack said dumped animal carcasses heightened a person's risk of illness, as bacteria from an animal's decomposing guts could be released, spread, and in certain conditions multiply in water.
He advised against anyone swimming in the river for at least 48 hours.
Anyone with open wounds could find their injuries infected and if they ingested any water they could become ill with vomiting and diarrhoea, he said.
In August, sheep carcasses, guts, skins and heads were among the two and a half tonnes of rubbish dumped in the river.
In the same month the Wairoa River was ranked as having some of the worst water quality out of all waterways in the Western Bay.
Dr Shoemack said any New Zealand waterway had some contamination but the level varied from factors such as weather events, tidal flow and animal contamination.
"It's bad enough when it happens in a natural event like floods but there's particular concern that some people doing it with intention are putting other people at risk," he said.
Federated Farmers Bay of Plenty president Rick Powdrell said the incident sounded "very much" like stock rustlers, which have been a significant problem in the region.
"It's the kind of thing they do, take the animals and butcher them and then dispose of the bodies somewhere," Mr Powdrell said.
"They often take the animals as quickly as possible, go somewhere more remote and dump the bits and head off with the meat."
Western Bay of Plenty District Council, which shared the cost of removing the rubbish, has erected signs in the area warning of fines of $500 and prosecution for anyone caught dumping.
