Authorities are investigating after an unidentified pink substance was discovered in the upper reaches of Whangamata Harbour.

Thames-Coromandel District Council Whangamata area manager Garry Towler said the discolouration was discovered by residents this morning. It was believed to be non-toxic, water-based paint.

Contractors had since pumped the discoloured water to the wastewater system for further treatment.

No animal or birdlife had been affected and the incident occurred in an area with limited public access and at low tide, Mr Towler said.

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It was cleaned up before high tide, but some minor discolouration remained on rocks and vegetation at the site, he said.

The investigation into the cause was being taken seriously.

"We are very disappointed to see this happening in such a beautiful spot ... we're investigating and following leads but are confident there's a human element involved in this. It did not get there by itself.

"Coromandel Peninsula takes this sort of thing very seriously. We have a low tolerance for deliberate acts of vandalism."

Anyone with information should call the council's Whangamata Area office on (07) 868 0200.