The department dropped 1080 in the Arthur Cleddau area and Bowen catchment area on Tuesday.
The use of 1080 in this instance protected vulnerable populations of whio/blue duck, pateke/brown teal, kiwi, and many other taonga native species, Fleming says.
"Because of a heavy seeding event [mast] earlier this year, predators such as rats and stoats are exploding in numbers.
"Without aerial control, our native species are under a significant threat and we may face local extinctions."
The operation mirrored the department's drop in the same area in 2017, which went ahead with no issue, Fleming says.
There was a 200 metre aerial buffer around the water intake in the Bowen catchment and for 200m upstream to the two feeder arms and a further 200m up both feeder arms, he says.
Cereal baits containing 1080 are hand laid within 50 metres of the main stem of the Bowen.
The department says 17 tourism operators were consulted as part of the planning for this operation.
Extensive research and monitoring in water catchments that have been treated with 1080 show that contamination is highly improbable when the current safety procedures are followed, he says.
The department says about 80 per cent of bird species are at risk of extinction because of introduced predators such as rats, stoats, and possums and aerial 1080 drops are effective at protecting wildlife and restoring forests.