In a media release, the Public Health Department said there was a possibility floodwater lying around the island could include faecal matter, which could enter the water supply and may have made streams and river mouths unsafe to swim in.
The release urged people to drink only boiled or filtered water and to seek medical assistance if experiencing symptoms of diarrhoea or skin irritation. It also emphasised the importance of washing hands with soap and clean water to stop the transfer of germs.
Residents have also been told to get their drinking water from water stations around the island, rather than relying on the cleanliness of their home supply.
Water stations marked with blue labels are considered safe to drink but those marked with a red label should be avoided.
Flooding is a proven cause of water and vector-borne diseases - infections transmitted by the bite of infected species such as mosquitoes and ticks. Diseases carried by mosquitoes can include dengue, zika and chikungunya. The Cook Islands currently has none of these diseases but each has affected the country at various times in the past.
The department warned against an increase in the mosquito population and highlighted the importance of keeping properties free of mosquito breeding sites.
Meanwhile, water problems continued on Rarotonga this week, with the Papua water intake suffering serious damage for the third time in as many weeks on Tuesday night.
Torrential rain has saturated the island for two weeks, with the first break coming only on Thursday. The sunshine gave the Water, Waste, and Sanitation Unit of the Ministry of Infrastructure Cook Islands (WATSAN) a chance to survey the damage.
On Thursday WATSAN issued a statement saying there had been disruptions to the water service in Nikao, suspecting that a blockage of the Avatiu intake was to blame.
They estimated it would take a day to repair the broken Papua intake, warning that there would be disruptions to parts of Arorangi and also to the south side of Rarotonga. The release said a number of intakes were once again blocked.
The presence of sediment in the water first caused alarm last week, with WATSAN advising all residents to get their water from approved water stations around the island.
Health ministry director of funding and planning Roana Mataitini said the health risks from sediment in the water depended on the type of contamination and on the quantity of sediments present.
He said the ministry regularly carried out bacteriological tests. on water stations throughout Rarotonga, following World Health Organisation water quality standards.
Meanwhile, Water Works have continued to flush out pipelines around the island to get mud or debris out of the water supply.
Water problems are expected to persist while heavy rain continues.