Controlled Area Notices have been issued for the three affected suburbs, which means movement of fruit and vegetables in and out of these zones is restricted.
Fruit was also being collected for examination and in some cases, disposal.
"More than 10,000kg of fruit has been collected in the bins placed in the three affected response regions and disposed of," Hutchings said.
"Additionally, a significant amount of fruit - around 800kg - has been gathered from properties within the A zones for each of the three responses and examined for larvae, without any findings.
"All the flies have been found in traps, which are very sensitive and an internationally proven method of surveillance," he said.
"If there is a breeding population present, there is a high likelihood of finding it as the response continues over the coming days."
The first fly to be detected was a single male Queensland fruit fly in Devonport on February 14. Four more have since been found in traps in Northcote.
Three single male facialis fruit flies have been found in traps in Otara.
If either of the species became established in New Zealand, officials said it would have serious consequences for New Zealand's horticultural industry.