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Cadbury communication manager Daniel Ellis told the Otago Daily Times last week that the roof on the four-storey building was being replaced as part of the factory's $51 million upgrade.
"We are not replacing the roof because of an issue with asbestos."
The spokesman said asbestos was commonly used in buildings of the factory's age and "a specialist asbestos removal company" had been engaged to remove the material and dispose of it.
"Asbestos is safe when sealed and managed in accordance with the appropriate safety standards and we have managed the site to these standards."
The factory is being converted into a "centre of excellence" and a portion of the roof is being raised to allow for a new, larger caramel cooker.
The factory is to get a new Coloursteel roof and that part of the upgrade is expected to be completed by late May.
Cadbury did not respond to questions about the quantity of asbestos being removed or where it was being disposed of.