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The council wanted use the company to process its household food waste collection.
The council's group manager of planning and infrastructure David Langford said its submission supporting Remediation NZ was made two years ago when it was only aware of minor issues at the site.
"We supported a regional organic waste processing facility as this was in line with our Zero Waste vision. But we were also clear that our support was conditional on the facility meeting environmental best practice standards and that any environmental impacts were minimised and properly managed."
Langford said more serious environmental concerns had been raised about the site over the past two years and it was clear the expected standards were not being met which was a major factor behind the council decision to transport food waste to Hampton Downs.