Hopkins said the majority of toxins used against them today, such as 1080 poison and anticoagulants, were "broad spectrum" - meaning they kill everything - and many could linger, entering food chains and affecting other species.
Such toxins were controversial and fuelled public resistance, but presently there were no other alternatives, with trapping still too costly to use on the scale needed.
"If we have a species-specific toxin it would make large-scale control much more socially acceptable and therefore help achieve national predator freedom."
Other benefits of a possum-specific toxin included not having to lock up dogs or restrict livestock, and that it could be used where existing agents couldn't, such as food warehouses, schools and zoos.
The scientists will be drawing on a technology developed by the pharmaceutical industry called genome mining, commonly used to discover human therapeutic targets suitable for drug development.
"We are flipping it's use around to discover possum-specific genes - their Achilles heel - that are suitable for lethal intervention to which possum-specific toxins can be developed.
"Using novel applications of innovative pharmaceutical technologies, we will identify targets in the possum to which we will develop, for the very first time, possum-selective poisons that have little or no effect on non-target species."
Using the approach toward toxins for vertebrate pests was a world first, he said, and would drive a new understanding of possum genetics, pharmacology and toxicology, creating a new and innovative platform technology.
Conservation Minister Maggie Barry has described genetics as the "next frontier" for pest control, despite the Cabinet briefing highlighting that iwi groups and some community sectors may be opposed to the technology.
NZ's possum plight
• Introduced into New Zealand in 1837 to establish a fur trade, and now considered a key pest.
• Notorious for ravaging native forest canopy, competing with native birds for habitat and eating their eggs and chicks, and spreading bovine tuberculosis.
• It's estimated they eat enough pasture to cause an annual $35 million loss in farm production, and cost government agencies a further $100 million in pest control spending.