The Ministry for Primary Industries has ordered an independent review of its biosecurity systems.
A Queensland fruit fly was spotted in the Devonport area of Auckland last week, and then a second type of fruit fly was found in Ōtara yesterday.
The pests pose a significant risk to New Zealand's $5.5 billion horticulture industry.
Bactrocera facialis - the facialis fruit fly - found in the South Auckland suburb is a different species to the Queensland fruit fly and is a separate incident to that in Devonport.
The facialis is native to Tonga and is known to affect crops of capsicum and chilli. However, it appears to be less harmful to other fruit and vegetables.
Ministry for Primary Industries director general Ray Smith told Morning Report he would be bringing in an independent expert, likely from Australia, to do a short review of New Zealand's border biosecurity to see if there was any holes in the system.
"I think it's prudent to have quick look and say ... 'are there any gaps, and if there are any let's find out and let's just go and fix them'."
The review would take about a month, Mr Smith said.
The facialis fruit fly was less of a risk than the Queensland fly because it targetted fewer types of crops and preferred a hotter climate and was unlikely to survive winter, Mr Smith said.
"But we just don't want to take the risk that it could establish in a pocket somewhere and cause damage to either local crops or in people's gardens."
MPI staff were out in Ōtara yesterday and would be again today dropping off leaflets letting people know what they needed to do to help eradicate the flies.
They would also be putting up signs in the area and distributing bins to residences in the Zone A area - houses within 200m of where the fruit fly was found - for people to put fruit and vegetable scraps in, Mr Smith said.
He said more traps would also be put into the area.
The Ōtara Market, held on Saturdays, were outside the danger zone and would be unaffected, but lots of MPI staff would be there talking to residents.
"One of the big things is going to be making sure we have a diversity in communications, languages, so that people can understand what we're talking about.
"Really the big risk is people taking vegetables and fruit out of the area.
"So the key thing with this is education. So signage, leaflets, talking to people on the ground, talking to local businesses."
Biosecurity Minister Damien O'Connor is cutting short a trip to Dubai and travelling to South Auckland this morning to help respond to a fruit-fly incursion.
Ōtara and Flatbush vege shops not contacted about latest fly found
RNZ visited eight shops selling produce around Ōtara and Flatbush yesterday - none of them had been contacted yet about the discovery of a second species of fruit fly.
Just off East Tāmaki Road, customers are spoilt for choice when it comes to fruit and vegetables.
But just around corner the facialis fruit fly has been discovered. This after last week's discovery of a Queensland fly.
For grocer Amrit Singh that is a worry.
"It's health and safety right, so it's something we should be looking at.
"[We need to know] what's happening and where it all started ... so we can get to the bottom of it."
Mr Singh has been selling fruit and vegetables in Ōtara for the past decade.
His store is located in Zone B of the surveillance area.
Mr Singh said fresh produce played an important role in his business.
"When people come and buy the fruit they buy other stuff with it," he said.
The first Mr Singh heard about the second fruit fly in Auckland was when RNZ told him about it.
Less than a week ago, a Queensland fruit fly was spotted in Devonport, sparking a massive biosecurity operation to check fruit and set traps.
Now, like Devonport, parts of South Auckland will now be subject to restrictions governing the movement of fruit.
MPI said the insect was known to affect capsicum and chilli plants but appeared to be less harmful to other fruit and vegetables.
One grocer off Te Irirangi Drive - also in zone B - said she thought MPI would have given fruit and vegetable stores more information and earlier.
Customers told RNZ they did not expect a second fruit fly to be found in Ōtara.
"If they found one I'm pretty sure there might be more around," one woman said.
MPI said it was setting more traps in Ōtara to check whether the facialis was a lone specimen or whether there was a population.