The University of Otago's director of genetics, Peter Dearden, said feral bee colonies were responsible for most of the pastoral, horticultural and cropping pollination, but in the North Island the varroa mite had decimated the population.
Dr Dearden said with the south of the South Island still varroa-free, there was time for scientists to pool their knowledge and skills before production fell, and breed a bee that was tolerant to varroa, productive and which would eventually restock the feral population.
He envisaged a joint effort involving scientists from Plant and Food Research (CRRT) (formerly HortResearch and Crop and Food Research), AgResearch, the University of Otago and industry that applied existing breeding, genetic and production skills to bees.
"We have excellent bee researchers in New Zealand.
"It is time we got together and worked to breed a bee that is tolerant to varroa."
Farmers and horticulturists also needed to be made aware a serious problem was looming which would affect their business.
Dr Dearden said some breeding work had already been done, but the resulting bee was not as productive as traditional honey bees.
Breeding bees the traditional way was also slow, taking a year per generation, but with AgResearch's gene selection expertise the process could be accelerated.
Dr Dearden said the key issue for New Zealand was the impact of varroa and ensuring the decimated feral bee population was restocked.
The bee's role in primary production was taken for granted, he said, evident by the experience in the United Kingdom and the United States where bees were disappearing at an alarming rate.
It was not known why.
The mysterious disease colony collapse disorder (CCD) was thought to be one reason, but it was also thought bees were being killed by exposure to chemicals.
As a result, honey production had fallen dramatically and beekeepers were being employed by crop owners to put hives near their crops so they can be pollinated.
A Varroa Planning Group report calculated the impact of varroa on the South Island honey bee population at 2003-2035 at a "middle" case cost scenario of $314 million, but a range, depending on the severity, from $198 million to $433 million.
The report said the impact would affect various industries differently, but once stabilised it calculated the annual cost to the pastoral sector at $234 million, beekeeping $1.07 million, horticulture $0.96 million and arable industries at $1.57 million.
Grasses and cereals were generally wind pollinated and floriculture had little need for honey-bee pollination while viticulture and some vegetables had a relatively minor reliance.
The sectors most dependent on honey-bee pollination were major horticultural crops such as kiwifruit, pasture clover, small seed and vegetable seed crops.
"For many of these there may be minimal crop set without adequate pollination.
"For others, production may take place but crop yield, size, quality and-or seed development may be adversely affected and-or the season may be delayed," the report said.
Extra costs would be incurred from having to use greater amounts of artificial nitrogen and more regular clover reseeding.
But, in summer in dry regions, there would be an annual additional cost from a 3.5% loss of production in sheepmeat, wool and beef from lower pasture growth and quality.
For beekeepers, the varroa outbreak has added $40 a hive a year to their management costs which would be added to the cost they charge for pollinating crops.
Dr Dearden said New Zealand could end up following the US model where bees were moved from coast to coast pollinating crops because there were no feral bee populations left.
Beekeepers carried a disproportionate amount of risk compared to other sectors that benefitted.
The National Beekeepers Association has estimated that for every $1 a beekeeper makes, other sectors benefit to the tune of $10, but Dr Dearden said that was part of the problem of getting industry funding.
"Farmers and horticulturists, they're the people we need to convince there is a problem."
But there was also a solution if there was buy-in by researchers and industry.
"We will have better, faster selection with molecular work looking at genes and I hope bees will escape and restock the feral bee population."
Dr Dearden has studied bees as part of wider genetic work.
He has looked at the genetic relationship between worker and queen bees and why queen bees were bigger, lived longer and bred, research he said had human implications.
Dr Dearden was also a director of Better Bees, a company based at the university which worked with beekeepers selecting bees suited to New Zealand conditions.
The unit was one of just two New Zealand groups which could artificially inseminate bees.