However, anti-chlorine group Te Vai Ora Maori-Clean, Safe Water for Rarotonga claims it is unnecessary to disinfect the water.
Instead they say government needs to investigate the “mud” entering the water system.
To Tatou Vai, the local water authority, commissioned water tests carried out by New Zealand-based accredited laboratory Watercare Services Limited in March and May this year.
Of the 40 samples tested, 33 contained E.coli and 21 of these had high or very high counts, the report said.
The tests did not identify the type or source of the E.coli.
“E.coli is an indicator that there is faeces in the water. If there are faeces then it is likely that there will be pathogens in the water as well,” To Tatou Vai said in a statement.
“The only acceptable level of E.coli in drinking water is zero.”
Te Vai Ora Maori says the samples were collected after heavy rain, which may have impacted the test results.
“You don't need a water expert to tell you that streams get muddy when it rains,” Te Vai Ora Maori said.
The weather preceding the March sampling round was heavy rain, intermittently widespread across Rarotonga for a few days, including on the morning of the tests, said To Tatou Vai.
It added the weather for the second tests in May was generally settled, but included some rain showers in the week before the sampling was done.
The tests samples were taken from randomly chosen sites around the island, including community water stations, intakes and a private home by To Tatou Vai staff.
The samples were sent by air the same day to Watercare Services using a standard sampling and “chain of custody” procedure to ensure verifiable results.
The results show 21 of the 24 samples tested in March this year had high or very high counts of E.coli. The May results were better – 12 of the 16 samples tested positive for E.coli but at lower levels.
The water authority only took samples from some of the community water stations. The results for the water station samples were variable.
“Overall, the E. coli counts are extremely concerning for a drinking water supply. All samples taken from the water intake sites tested positive for E.coli,” To Tatou Vai said.
Government earlier confirmed water disinfection following the completion of the Te Mato Vai project and chlorination is the favourble choice.
Te Vai Ora Maori said: “Chlorine won't 'zap the bugs'. For cleaner, safer, water, we need to investigate the 'mud' - we need to know what is in our soil. We need a water treatment system for (tropical) Rarotonga.”