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Testing by the Ministry for Primary Industries confirmed the infection at a plant nursery late this morning.
The ministry's myrtle rust response controller, David Yard, said no plants would be moved and they were preparing to treat the area with fungicide.
Mr Yard said MPI staff would inspect the surrounding area in a 500 metre radius.
The infectious fungal disease, which puts native plants such as pohutukawa and rata at risk, was discovered two weeks ago in Kerikeri in the Far North.
Other at-risk species include feijoa, gum and bottlebrush.
Mytle rust is believed to have been blown over from Australia.
Anyone believing they have seen the fungus on plants in New Zealand were asked to call MPI on 0800 80 99 66.
It was important for people not to touch the plants or attempt to collect samples as this would spread the disease.