An area of 6300ha of public conservation land in the Otahu catchment near Whiritoa will have a 1080 operation.
Starting this month, the aerial pest control is part of the government's nationwide 'Battle for our Birds' 1080 operation.
Otahu is largely forested, and drained by the Otahu River and tributaries to the Otahu estuary, which covers about 110ha providing significant vegetation and wildlife habitat.
"There have been an increasing numbers of rats, stoats and possums in this area.
"We want to give native animals a decent fighting chance," biodiversity ranger for the Hauraki area, Leo Pickering says.
Another 700ha of private land in the nearby Mataora catchment will also be targeted.
The land belongs to Ngati Porou iwi who have asked to be part of the predator control operation, DOC said.
"It is the second time we have done an operation for them," Mr Pickering says.
DOC says it has established a 100m buffer zone around properties after discussions with affected owners.
"Also there will be no chance of contamination in the water supply in Whiritoa, Waihi or Whangamata and the operation is well away from the Otahu estuary behind farmland."
Application rate of pesticide is usually around 1.5 to 2kg of bait per hectare with each bait containing .015 per cent active ingredient.
The rest is a cereal bait. "We are dropping about four to six pellets per tennis court size. There is a lot of misinformation about 1080 but the technology we have nowadays, such as GPS etc., we can really refine areas we are targeting.
"We know 1080 is not a final solution and there is a certain amount of by-kill from it - which is unfortunate - but it is minimal compared to native animals dying of predation every night," he said.
Both operations are part of a Mountain to Sea pest control campaign led conjointly by DoC and Waikato Regional Council. The regional council will back up DOC's aerial operation with ground pest control.
"On top of this aerial control [in Mataora], WRC is exploring carrying out ground control on around 4600ha of land adjacent to the [Otahu] area DOC is planning to treat aerially," a council spokesman said.
"We've directly contacted most of the private landowners involved in the proposed ground control area and those spoken to are supportive of it," he says.
Both areas will be signposted as part of normal operational procedure, and affected people will be consulted before the operations get underway.