Struggling Auckland oyster farmers will receive financial support from Watercare after a fault at its Warkworth wastewater pump station left their farms contaminated and unable to harvest.

Watercare estimated the overflow volume was about 1200 cubic metres, but did not know how much had reached the harbour.

The fault was not flagged by Watercare's internal alert system.

From Wednesday afternoon until Thursday morning, wastewater entered the adjacent stormwater pond and then flowed into the Mahurangi River.

Watercare confirmed on Monday in a statement that it was discussing the issue of financial support with Aquaculture New Zealand, which was acting for the oyster farmers.

Chief executive Jamie Sinclair said Watercare was deeply sorry.

"We understand how serious this is - it's caused disruption and hardship for people whose livelihoods depend on a clean harbour. We are genuinely sorry and we're committed to making it right," said Sinclair.

Watercare said the pump station was stabilised and normal operations were restored on Thursday, with the combined wastewater and stormwater pumped from the stormwater pond back into the pump station on Thursday and Friday.

The agency said a thorough clean-up of the area was carried out over the weekend and the pond was refilled with clean, unchlorinated water in line with advice from Auckland Council's freshwater ecologist.

It said testing had since shown the pond water was now within safe levels.

Watercare said the overflow was a unique incident caused by a technical failure following a power surge, which disrupted operations at the Warkworth site.

It is understood the surge tripped the pumps, causing the pump station's storage tank to fill.

Sinclair said the cause of this overflow was different to previous issues that were caused by rainfall and growth putting pressure on existing infrastructure, and which was being addressed by infrastructure upgrades.

"This overflow was caused by a power surge and compounded by our alert system not working as we would expect, which meant it was not identified as quickly as it should have been."

Sinclair said two investigations were underway - one looking at the cause of the power surge that tripped the pumps and resulted in the overflow; while the second review would look at why alarms did not immediately alert Watercare to the problem.