The deadly varroa mite has been found in beehives in Invercargill and Dunedin.
The parasite kills unprotected bee colonies has been spreading south since it was first identified in the North Island 10 years ago.
It reached the top of the South Island in 2006. Attempts to contain it in Nelson and Marlborough were abandoned in late 2008 when the mite was found in North Canterbury.
Federated Farmers Bee Group chairman John Hartnell says the latest infestation was inevitable after the mite reached Queenstown in 2010.
"It's taken quite some time to work its way south - we were able to hold it at bay for a couple of years at Cook Strait. But in the end it snuck over to Nelson in 2006 and it's progressed from there."
Mr Hartnell says the only part of New Zealand which can now claim to be free of the parasite is the Chatham Islands.
He says there are few wild beehives left in New Zealand and believes they will all be wiped out over the next two years.
"The varroa mite is a very effective killer and if man doesn't intervene by putting some sort of control method in, then the hives are basically killed off."
Mr Hartnell says treating hives for varroa costs about $50 per hive and must be done about three times a year.
National Beekeepers Association president Barry Foster says dealing with varroa will be difficult and expensive and the Government should step in to help the industry with research and funding.
Mr Foster says the country's exports, income and food supply depends on finding solutions that fit the New Zealand situation.
There are 420,000 hives in New Zealand, kept by 3750 beekeepers.