The discovery has drawn criticism from Horticulture New Zealand, which said it was "unbelievable and unexpected" for another fly to be detected so soon after the last one.
The find brings the total number of Queensland fruit fly detections in New Zealand to three in fewer than two years. Before May 2012, there had not been a single detection for 16 years.
Horticulture NZ chief executive Peter Silcock he had confidence in the system to detect fruit flies at a very early stage.
"But we do have to urgently look at how we are managing the biosecurity risk, so we don't keep finding this pest in our traps," he said.
"This is a pest that we don't want because it will impact on our ability to grow things, export produce and on the 50,000 jobs this industry provides across New Zealand. It is in everyone's interest to keep this pest out."
Green Party biosecurity spokesman Steffan Browning said the discovery raised serious questions about New Zealand's biosecurity preparedness.
He said MPI needed to explain why it thought the fruit fly was a new incursion.
"Given that the last fruit fly was found in the same region only a few months ago it seems likely there is a connection.
"If it is the case that this fruit fly is linked to the previous incursion, then it raises serious concerns about MPI ending their January campaign early, before ensuring there were no other fruit fly in the region."
Labour Party primary industries spokesman Damien O'Connor said the finding showed there was a systemic problem which the ministry had been unable to fix.
"There must now be a complete review of MPI's response. If insufficient resources were put into the investigation into how these flies came into New Zealand, then the ministry must change the way it approaches biosecurity incursions."
MPI said it had responded promptly and field teams were already setting up additional traps to determine if other fruit flies were present.
"As in January, it is vital we find out if the insect is a solitary find or if there is a wider population in Whangarei," Mr Coleman said.
The controlled area was an important precaution while MPI investigated whether any further fruit flies were present in the area, he said.
"The Whangarei community were immensely supportive of our efforts earlier this year and we anticipate they will be again. It is, of course, disappointing that this situation has recurred."