A 1080 poison operation conducted in conjunction with farmers and covering roughly 3000ha in three blocks along the eastern face of the Kirkliston Range had knocked numbers back significantly in July.
September's shoot will be the next major assault on the pests, which are starting to cross the river and migrate south into Otago.
Environment Canterbury has a defined wallaby containment area that stretches from Otematata to the coast along the north bank of the Waitaki River and runs roughly 100km north.
The Kirkliston Range Conservation Area, one of Doc's highest-value conservation areas, is in the southwest corner of the containment area and sits above farms that run down to the Hakataramea Valley, immediately on the north side of the Waitaki River.
Mr Theobald said the helicopter shoot was expected to slow down the wallabies' "re-invasion" of that area.
"They're non-stop - they're non-stop.".
Environment Canterbury (ECan) biosecurity team leader Brent Glentworth said ECan's advice to landowners was poison was the best way to control wallabies, because they were often in difficult-to-access areas and could become gun shy.
In total, 4500ha was poisoned this year.
Still, landowners needed to keep pressure on the pests with shooting as a "post-poison secondary control".
Doc media adviser Fiona Oliphant said the department was also planning a ground poisoning operation for wallabies in the Studholme Scenic Reserve near Waimate this spring.
Outside of the Kirkliston Range, Doc had conducted aerial shooting operations at Mount Studholme Conservation Area in the southern part of The Hunters Hills in June, where 973 wallabies were shot; at Hunter Hills Conservation Area near Mt Nimrod/Kaumira in
the northern part of The Hunters Hills in June, where 575 wallabies were shot; and at the Chetwynd Conservation Area near Fairlie this month, where about 400 wallabies were shot.
However, Mr Glentworth said he was concerned that numbers could be taken as a measure of control.
A farmer could shoot 2000 wallabies and still have a problem, he said.
"Just like rabbits, it's not about how many you shoot, it's about how many you leave behind."
hamish.maclean@odt.co.nz