Outbreaks of the wind-born rust were followed by a team from the ministry removing all affected plants. Myrtle rust has previously been found in Te Puke, with 18 confirmed sites in the Bay earlier this year.
The ministry did not disclose the locations of myrtle rust outbreaks.
The co-owner of Decor Gardenworld in Bethlehem, Ginny Clark, had not been notified about the two cases in Bethlehem.
She said they had very strict systems in place, including checking for the disease every day and preventative spraying. Susceptible plants were sterilised before delivery.
''Everybody needs to be aware but unfortunately it could be in parks and reserves or bush areas ... the horse has potentially bolted.''
Ron Mossop of Mossop's Honey said their hives had all been moved out of the city.
He said the impact of myrtle rust on manuka had yet to be proven.
''They are pretty hardy plants. We have not felt the impact of myrtle rust yet.''
Grant Tennet, whose Te Puna citrus nursery was not affected because citrus was not a myrtle species, believed the ministry was hitting its head against a brick wall in trying to control it.
He said the disease could be managed in nurseries and commercial orchards.
''But out in the hills who will be spraying?''
The good news was that feijoas were a lot more resistant to myrtle rust, he said.
