Dr Miller said people could become ill with gastroenteritis after swimming in the water. People with cuts or scratches on the skin were at risk of infection.
A sign has been erected at the site and Dr Miller said he hoped people would take note.
"We haven't had any reports of anyone [becoming sick] from there. I think it's more about making people aware of the risk," he said.
Dr Miller said he was not aware of the exact cause of the contamination but areas like Kaiate Falls, which were in isolated areas with more animals and septic tanks, were more likely to register poorer water quality.
The Bay of Plenty Regional Council regularly monitors the district's water quality and results can be found on its website. Kaiate Falls is currently listed as unsafe for swimming.
The warning joins another health advisory to not consume shellfish from the Bay of Plenty coastline due to paralytic shellfish poisoning.
Shellfish such as mussels, toheroa, pipi, tuatua, cockles, oysters, scallops, catseyes, pupu and kina (sea urchin) remain unsafe to eat.
People could experience poisoning symptoms including numbness and tingling around the mouth or face; difficulty swallowing or breathing; and in severe cases, paralysis and respiratory failure.
