Two mites were found on bees from University of Otago research hives on Monday night. The parasite was earlier found by a hobbyist beekeeper in Invercargill.
Until now, the varroa mite - a parasite that destroys bee colonies by transmitting viruses from adult honey bees to larvae - had spread throughout New Zealand but had not been confirmed south of North Otago, other than in parts of Central Otago.
The mite was first found in New Zealand in 2000.
Otago University department of biochemistry Associate Prof Peter Dearden, who heads bee research at the university, said it informed the National Beekeepers' Association as soon as the mites were found.
The find indicated there was a "low level" infestation of varroa in the Dunedin area, which had spread to the university's hives, Prof Dearden said.
"We haven't moved our hives and we haven't worked in areas where there have been varroa mites, so we are pretty sure that we haven't brought the mite into Dunedin."
It was not clear how the mite got to Dunedin, he said.
"It could be a beekeeper has carried one on their suit, or it could be that they have just naturally spread down the country."
National Beekeepers' Association of New Zealand Otago president Allen McCaw said confirmation the varroa mite had spread to Dunedin and Invercargill did not come as a surprise.
Now that it was here, it would spread quickly, which meant there would be added costs and labour associated with treating hives for varroa mites, Mr McCaw said.
The cost of treatment, between $20 and $40 a hive, would be a "significant" burden for beekeepers.
The extra cost could cause some hobbyist beekeepers to give up, he said.
The added labour also meant some commercial beekeepers may have to reduce hive numbers.
"A lot of beekeepers have found that whereas they might have been able to ...
manage anything up to 1000 colonies on their own [before varroa], they find that very quickly comes down to 500 to 600."
Now varroa had been found, beekeepers would need to be vigilant and do extra testing.
"It's not a situation to panic about, but it's not one you can ignore," he said.
Prof Dearden said varroa would have a larger impact on feral bees, which would not be treated for varroa and would therefore be "wiped out".
"That's a lot of bees that we are going to lose over the next year, year and a-half."
He said once varroa set in, people living in the city would probably notice fewer bees in their gardens, which could result in fewer fruit trees and vegetable crops being pollinated, reducing crops.
People could also notice an increase in the number of bumblebees, which are not affected by varroa.
