This follows concerns that miles of piping in Stage One of Te Mato Vai, a plan to bring potable water to everyone on Rarotonga, will have to be pulled up and replaced.
The Chinese Civil Engineering Construction Company, or CCECC, completed Stage One last year but there have been reports it starting leaking immediately.
A spokesman said the ministry was aware of quality concerns with respect to the ring-mains built by CCECC.
New Zealand's role is now building and upgrading the water intakes and this is progressing well.
He said all partners remain committed to seeing Te Mato Vai succeed in achieving a quality water system for the Cooks.
Overall, New Zealand is contributing $67.7 million in development assistance to the Cook Islands in the current three year funding cycle.
The spokesman said the bulk of this is for infrastructure projects and $13m of which is earmarked for asset maintenance and MFAT is happy for this to be used for any repairs to water ring-main.
- Radio New Zealand