A lawyer acting for Waiwera Water, Mike Whale, said the distributor had promised to pay for the consignment but "suddenly changed their tune and refused to pay, allegedly because the water had excessive boron levels".
"Waiwera have proof that [in] the shipment of 10 containers that went up to Dubai, there wasn't excessive boron levels. Waiwera is working through the issues with this distributor. We consider it a private commercial matter."
The Herald on Sunday requested Waiwera water testing documentation but this could not be provided by deadline.
A New Zealand Trade & Enterprise spokesman said the Dubai Trade Commissioner spoke to Waiwera and the distributor after learning of the dispute.
The Dubai-based distributor told the Herald on Sunday it was "very confidential between myself and the company". "Still we are partners. That's all I can say. You can ask any questions for them."
Water New Zealand chief executive Murray Gibb said boron was a naturally occurring element commonly found in geothermal areas.
According to the World Health Organisation, a small amount of boron is permitted in drinking water but it can be toxic at high concentrations.