The destructive Varroa bee mite has beaten MAF's control line and has been found in a log shipment at Pauatahanui, north of Wellington.
The mite was found in a colony of wild bees inside a hollow log shipped from the Far North - but MAF was not alerted until 12
days later.
The tiny pest is capable of destroying bee colonies and is a serious threat to the beekeeping industry.
The Ministry of Agriculture and Forestry operates a control line between Taranaki and East Cape that is designed to restrict the movement of live bees and contain the mite in the upper North Island.
This is not the first time the mite has spread beyond the line.
MAF biosecurity spokesman Stephen Olsen said the logs arrived at the Pauatahanui mill on January 14.
It was 12 days before MAF was told and was able to contain the situation. MAF immediately destroyed the host bee colony.
Other measures included restricting live bee movement by beekeepers within 5km of the find and treating all beehives within that radius against the mite.
National Beekeepers Association president Don Bell said it was disappointed at the find.
"Beekeepers have fully supported the movement restrictions," he said. "The NBA has also done its best to raise public awareness of the risk of live bees being accidentally transported from one part of New Zealand to another."
MAF and the association said the lower North Island had been Varroa free until now.
"We can only hope this is an isolated incident," Mr Bell said.
"Beekeepers are making progress in learning how to deal with the damage the Varroa mite causes and we are encouraged an NBA member helped to alert MAF to the suspected find."
Mr Olsen said the transport company would be spoken to as part of MAF's investigation.
He could not say whether it would face a penalty.
- NZPA
nzherald.co.nz/environment