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Biosecurity officers intercepted the larvae last month in undeclared food from a holiday group at Auckland Airport, says Biosecurity New Zealand passenger manager, Craig Hughes.
The larvae were found in chillies following x-ray screening of the tour leader's baggage. A caterpillar was also detected in some garlic bulbs carried with the undeclared food.
"Many horticulture crops are susceptible to attack by fruit fly. Affected fruit and vegetables could be inedible or subject to trade restrictions if the pest became established in New Zealand.
The tour leader received a $400 fine for failing to declare the food package.
The intercepted larvae were believed to be Malaysian fruit fly, which has invaded a number of Pacific islands. The species attacks more than 60 types of fruit and vegetables.
Hughes says biosecurity officers are on high alert for fruit fly following recent outbreaks in Tasmania and Adelaide.
Biosecurity New Zealand has made more than 10 fruit fly interceptions at the border this year.
"This is about protecting New Zealand from an invasive pest that could seriously harm an industry worth $5 billion in domestic sales and exports."