The city's wet industries told council what loads they were going to put into the treatment system during the year, and three or four times a year council staff monitored those industries on site.
Mr Hughes said council just doesn't know which of the industries was responsible for pumping the abnormally high levels of protein into the system.
But he said council would work with those industries to implement a new regime of random testing.
"The point is we can't guarantee this sort of thing won't happen again, but we want to be checking more often and randomly and will be meeting with those industries in the new year," he said.
He said closing the treatment plant for a period was not an option.
"We could divert the untreated waste directly through the South Beach outfall into the sea, but that's just not an option."
As the stench intensified, council staff have been dosing the ponds with odour-treating chemicals as well as spraying the pond surfaces each day.
The aim of the chemicals targeting the stench is to improve the oxygen levels in the top metre or so of the ponds before Christmas. Similar treatment is happening at the Beach Rd pumping station before the waste reaches the ponds.
Mr Hughes said the extra processes added to the ponds were not impeding the bio-augmentation (bacterial) process already in place. He said gains were being made until the unexpected waste was dumped into the system.
Yesterday Nic Peet, Horizons' group manager of strategy and regulation, visited the ponds with Mayor Annette Main, and said his council was supportive of the approaches the WDC had taken.
"The formal warning from us puts the council on notice but we're comfortable with what it's doing to resolve this problem," Mr Peet said.