Mr Guy thanked Whangarei people in advance for their co-operation - "You were fantastic last time" - as MPI dealt with the repeat biosecurity alert.
Kerikeri Fruitgrowers' Association chairman Rick Curtis also thanked city residents for enduring biosecurity precautions for the second time this year.
But, while supporting "the MPI guys on the ground", he said growers were very disappointed and concerned about fruit flies getting into the country.
Biosecurity entry protection needed tightening as the present "ambulance at the bottom of the cliff" policy was unsustainable, Mr Curtis said.
MPI deputy director general compliance and response Andrew Coleman said it was believed the new find was unrelated to the January incident and it was a coincidence the two insects were found in the same area over two months apart.
MPI experts were confident both fruit flies had not arrived in New Zealand as adults but as eggs or larvae. The fly's life cycle involves two months of development from egg to the adult stage in which the male survives for a month.
The new find on Tuesday was high on Mt Parihaka, and looking down from the trap site to the Town Basin marina it was tempting to assume the fruit flies had crossed the Tasman on a private yacht, Mr Coleman said.
"But that scenario is too simplistic," he said, explaining how MPI staff would check with residents to see if the insects had arrived with someone returning by air from overseas, in overseas mail or with other overseas cargo.
Up to 120 MPI and Quality Assure staff who worked on the biosecurity threat in January are expected to return to Whangarei. A mobile laboratory used to analyse fruit and vegetables from zones around where the pests were found was to be back in the city yesterday.
The two Whangarei finds this year were the fourth and fifth fruit flies detected in New Zealand. The first was at Onerahi in 1995, the second at Auckland in 1996 and the third at Auckland in 2012.