Whangarei harbour is closed for swimming and shellfish gathering for a month, after days of heavy rain overloaded the city's sewerage system.
But the council says it is gradually getting a grip on the problem.
It says the main treatment plant went into extreme bypass mode for a couple of hours, spilling partly treated waste into the sea.
But it says the spill was only 14% of what it would have been if the disinfection system had not recently been expanded.
Council waste manager Andrew Carvell says by May next year further expansion will make the emergency bypass mode a thing of the past.