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The ''vile'' smell over Waikouaiti was caused by composted fertiliser, including chicken manure, being spread over a paddock, the Otago Regional Council says.
The council investigated after reports to its pollution line of a bad odour wafting over the township on Monday and Tuesday.
Council environmental monitoring and operations director Jeff Donaldson said contrary to some residents' belief, the odour did not come from the town's Mainland poultry farm, but a paddock next door.
A staff member discovered composted fertiliser had been spread on a paddock adjoining the factory by a landowner.
The property owner was being notified by the council and advised to plough the fertiliser into the ground quickly.
The odour had dissipated on Wednesday, as the wind direction had changed.
Anyone who was planning to put composted fertiliser on their land needed to be aware it was unacceptable for it to cause an objectionable odour beyond the boundary of their property, he said.
''If it does, you need to do something about it.''