The Ministry for Primary Industries says it is aware of nine batches of New Zealand honey products that have tested positive overseas for added sugar so far this year.
But an MPI spokesperson says re-testing of two batches using a more specific method indicated that at least some of those results were likely to be false positives.
GNS scientist Dr Karyne Rogers is heading the honey research project and she says beekeeping practices are also under scrutiny.
Apiarists have been warned to take extra care with the common practice of feeding sugar syrup to bees in late autumn or early spring before the honey flow starts to prevent starvation and boost hive populations.
Rogers says feeding too close to harvest can lead to C4 sugar showing up in the honey. "In poor nectar flow seasons bees are not collecting enough nectar to dilute the one or two sugar feeds they've been given."
Chair of the Bee Products Standards Council, Dr Jim Edwards, says although none of the positive results to date is believed to result from deliberate adulteration of honey with cane sugar, the industry is genuinely concerned about its reputation.
He says beekeepers in some regions have started feeding protein supplements to their hives to compensate for seasonal pollen shortages, and questions have been raised as to whether that practice could raise protein levels in honey and trigger a positive test result.
Concerns about adulterated honey have led to stricter policing of honey standards globally and Rogers says about $5 million worth of New Zealand export honey has been held back at overseas ports over the past two years.
"Countries start to get grumpy when they get more than one fail and they start to threaten to shut down access, or in the US they could shove (shipments) into a shed on the wharf and leave them there for a few months while they do rather costly and time consuming testing."
"A lot of the honey is good and should be treated as such and unfortunately because of the false positive issues there's a lot of grief for a few people."
Comvita, a major exporter of Manuka honey, declined to comment when asked if any of its products had been stopped at overseas after failing the sugar test.
Comvita CEO Brett Hewlett said it wasn't a major issue and all of the company's honey was routinely checked as part of its quality control system.
Two Canterbury companies whose honey failed the test are on the FDA's import alert "red list" in the US which means their honey can be subject to detention without physical examination.
Claridges Organic has had several shipments of Manuka honey stopped in the US and general manager Lawrence Heath says with 27,000 pottles of honey in each shipping container, it is a huge problem.
He firmly believes the test is at fault because rejected honey sent to a reputable German honey laboratory for re-testing got a clean bill of health. "The Germans came back and said 'hey your honey is totally normal'.
"I think we'll find down the track that Manuka in unique in ways that throws up these false positives when this particular test is used."
At present rejected honey can be destroyed, re-exported to another market, or returned to New Zealand for sale here.
An MPI spokesman says sugar feeding is an essential tool in the bee industry and because the flowering of nectar-yielding plants is unpredictable, it is impossible for beekeepers to completely eliminate all risk of C4 sugar ending up in honey.
Honey made by bees from sugar fed to a hive still meets the legal definition of honey. However if sugar is added directly to honey after it is removed from the hive, the resulting product is not classed as honey under the Australia New Zealand Food Standards Code and cannot be marketed as such.