The lone male fly was caught in a Ministry of Primary Industries (MPI) trap on Monday afternoon, with confirmation coming in late yesterday evening.
The fruit fly could have "serious consequences" for New Zealand's horticultural industry, MPI warned, with the possibility of damage to a wide range of crops, and restrictions on trade.
Mr Guy said biosecurity was his number one priority as Minister.
"This is an isolated incident and shows the system working as it should.
"In the last two years around 125 new quarantine inspectors and more detector dog teams are working on the frontline, and we have new x-ray machines installed at our international airports."
Both Labour and the Green Party hit out at the Government, saying the discovery was proof that cuts to MPI had led to "flimsy" biosecurity controls at the nation's borders.
Horticulture New Zealand warned of the threat to $5 billion horticulture industry and called for the reinstatement of mandatory x-ray screening of all inbound luggage at international airports.
A 1.5km circular exclusion zone has been set up by MPI, restricting the movement of fruit and some vegetables in Grey Lynn and taking in parts of Western Springs, Mt Albert, Ponsonby and Kingsland.
Eden Park and Auckland Zoo both lie inside the zone.
The restrictions are likely to be in place for at least two weeks, MPI said. Last year's fruit fly find in Whangarei saw restrictions in place for 20 days, and cost the country almost $1 million.
"These legal controls are an important precaution while we investigate whether there are any further fruit flies present," MPI chief operations officer Andrew Coleman said.
"Should there be any more flies out there, this will help prevent their spread out of the area."
He urged people to abide by the rules, saying previous operations had shown public support "is vital to success".
"We appreciate this will be inconvenient for the many people living in and around the controlled area, but compliance with these restrictions is a critical precaution to protect our horticultural industries and home gardens," he said.
Two Countdown supermarkets sit within the exclusion zone -- on Williamson Ave and Richmond Rd -- as well as a number of other local fruit and vegetable shops.
"It's an inconvenience for our customers but we absolutely recognise that Queensland fruit fly is a serious biosecurity risk and we're happy to help," a Countdown spokeswoman said.
"Customers who live in the quarantine area can still buy fruit and veges from our stores to eat inside the area, but they can't take it from our stores or their homes to anywhere outside the controlled area."
Auckland Zoo said the restrictions would not have any impact on bringing food in for the animals, but it was working with MPI on the disposal of waste fruit products.
A spokesman for the Cricket World Cup said MPI would supply specialist bins for fans to dispose of fruit and vegetables after the match between New Zealand and Australia on February 28.
The weekly Grey Lynn Farmers Market also falls within the cordon, but manager Louise Carr-Neil said it would still go ahead this Sunday.
"A lot of our growers are in Kumeu, they're able to bring fruit and veg into the market with no problem, but people who buy fruit and veg at the market, excluding leafy greens and root vegetables, won't be able to take it outside of that 1.5km radius," she said.
"Of course that's going to affect the market this week, and we're hoping it will be cleared up as soon as possible.
"But a lot of our customers are based very close to the market, and that exclusion zone is actually pretty big, so the market is going ahead as normal."
Grey Lynn Residents Association committee member Nicola Legat said she was concerned about the "economic impact on our local businesses", and said everyone was "anxious" about how long the restrictions would be in place for.
But she added: "I'm sure that Grey Lynn people will do their utmost to participate in whatever it is that we need to do."
Horticulture New Zealand president Julian Raine laid the blame for the fruit fly breach on "Australia's inability to control the pest" and urged the reinstatement of mandatory luggage x-rays at airports.
"It is not acceptable to go through this drama every summer. New Zealand horticulture deserves better protection."
Labour's spokesman for primary industries, Damien O'Connor, said the fruit fly discovery showed there was a "failure" at New Zealand's borders, and blamed Government cuts for leaving MPI short of experienced staff.
Green Party biosecurity spokesman Steffan Browning said the discovery showed New Zealand's biosecurity measures were "flimsy".
"We also have to question whether cuts to frontline biosecurity staff since 2012, when the fruit fly incursions began, have had an effect on the quality of screening."
By Patrice Dougan of NZME. News Service
