A member of the public discovered the infected plant on the Karamatura Trail at Huia, and reported it through the iNaturalist app, where the Department of Conservation confirmed it.
Myrtle rust was discovered in New Zealand in 2017, having blown over from Australia's east coast, where it has led to localised extinctions in myrtle species.
It has gradually spread across the country, appearing to particularly affect ramarama, a native shrub that grows 8 to 10 metres high.
Near the end of last year East Coast Department of Conservation ranger Graeme Atkins discovered mature ramarama dying from the disease - the first cases in the country of mature native trees dying, and sparking fears of localised extinctions.
Myrtle rust can infect hundreds of species in the plant family Myrtaceae, which in New Zealand includes mānuka, pōhutukawa, rātā and kānuka.
Once established on a host tree or shrub, it destroys new growth and soft tissues, in some cases eventually killing the plant.
To date, pōhutukawa have not been badly affected in the Auckland region.
Auckland Council's environmental services and regional parks teams are assessing the site before deciding what to do.
"That may include removing the infected plants to protect other plants or we may decide on taking no further action," natural environment delivery manager Phil Brown said.
People should not touch myrtle rust or come into close contact with the plant to prevent spreading the fungal spores.
People are encouraged to take photos and use the iNaturalist app, where experts can confirm the infection.