Peter Wimsett, council's manager of district strategy and development, said the problems prompted his council to begin planning for an upgrade of the water scheme.
"At the moment, we seem to be getting a lot of turbidity in the Pongaroa supply," he told the Dannevirke News this week.
"Pongaroa has a very large reticulated scheme. It's huge and rivals Dannevirke's scheme."
Wimsett said the problems with the water quality at Pongaroa come about because the chlorinator was close to the water source in the Puketoi Ranges.
Along with the very high turbid water from intake supply there was a low chlorine residual in the town reticulation network.
"The water has a long way to go to Pongaroa and we have been rebuilding the old sand filter and we'll treat the water for the reticulation before it gets to Pongaroa," he said.
"At the moment we are building a new treatment plant, with the work completed in the next week and then the filtration plant will be installed. We are still aiming to have this operational by July 31, subject to the weather."
Pongaroa's water will then be treated to the required drinking water standard and Wimsett hopes this will be the end of the ongoing water problems.
The new plant is being built at a cost of $600,000, with an additional $50,000 for an AVG filter.
The council has received a $393,000 subsidy from the Ministry of Health for the work.
Boil your water:
Until notified otherwise, Pongaroa residents connected to the town supply are advised to boil water before using it for drinking (including making of sachet juice/drinks), making ice, food preparation, brushing teeth and preparing infant/toddler formula.