Updated 3.33PM: Auckland's fruit fly scare has ramped up another level with the discovery of a third bug.

The single female fly was found in a lemon tree in Grey Lynn just days after a male fly was trapped nearby.

The Ministry for Primary Industries investigators visited the property where the latest fly was uncovered.

There they found lemons and plums containing 39 larvae and one pupa.

The Ministry says it has every confidence treatment will quickly and effectively eradicate this isolated population of the insect.

MPI chief operations officer Andrew Coleman says the discovery is worrying, but shows their system is working.

We would rather not find any fruit flies, whether they be larvae, pupae, or live insect," he said.

Coleman says they are putting out bait stations with an effective insecticide to catch the flies.

"It's common in pet flea collars, so for those who have pets, it's the insecticide that actually kills the insects."

An additional export restriction zone now extends for 3.5 kilometres from the site of the second detection.