The Wellington Regional Council says the Waiwhetu Stream is more polluted than it first thought.
Waste was excavated from the banks of the stream in Lower Hutt last October during the council's clean-up of the region's most polluted waterway.
Material that the council believed was free of toxins was dumped into a landfill not certified to receive toxic substances. However, lead pollutants had flowed further downstream than expected, and a lower section of the stream has now been reclassified as a toxic site.
The council says the waste has now been sent to a landfill with a special lining that stops the contaminants leaching out.
Up to 25,000 cubic metres of material will need to be removed from the stream, double what was initialy estimated. The council hopes to finish the clean-up by September.