It was first found in hives in Invercargill and Dunedin - both tended by the same Dunedin hobby beekeeper - last month and then a few days later two mites were found in University of Otago research hives.
Until last month's find, Dunedin was the last major centre in New Zealand showing no sign of the varroa mite. The parasite destroys bee colonies by transmitting viruses from adult honey bees to larvae.
National Beekeepers' Association of New Zealand Otago president Allen McCaw said tests since the initial find suggested most hives in Dunedin were infected.
The mite had been found in hives throughout Dunedin, including in the Town Belt, Leith Valley, Otago Peninsula and the Taieri Plain, he said.
The wide spread of varroa did not come as a surprise.
"It's always somewhere ahead of where you are looking.
"You only look when you notice it and when you notice it, it's probably [spread] a couple of hundred kilometres further."
The infestation was still at "relatively low" levels, but it was "only a matter of time" before mite numbers became more noticeable.
By spring, most beekeepers would need to be treating their hives for varroa.
After that, wild bees would be hit hard by the parasite and begin to abandon their hives and shift to commercial hives, bringing varroa with them, meaning more treatment would be necessary.
That would be when the public might start noticing a drop in the number of bees, which could make it harder for people growing fruit and vegetables to get their plants pollinated.
Treating for varroa would cost beekeepers between $20 and $40 a hive and this cost and the added labour could cause some hobbyists to give up on beekeeping, he said.
Betta Bees Research manager Frans Laas said the level of infection in Dunedin suggested varroa had been in the city for more than a year.
It normally took about 18 months for the infestation to reach an "acute phase", when the wild bee population would start collapsing and any bees in untreated hives would die.
Mr Laas is researching ways to breed bees which are both resistant to varroa and commercially viable.
At present, it was possible to breed "hygienic bees" which were resistant to varroa, but they did not produce enough honey to be viable.
