This corresponded to a loss of native biodiversity equivalent to $1.3 billion.
Vertebrate pests such as rats, possums, stoats and wild pigs were costing the primary sector $1 billion per year - and the indirect cost could be as high as $3.3 billion - or nearly 2 per cent of GDP.
The report highlighted the need for improved tools and technologies, such as fertility suppression and biological control, to counter increasing pest resistance and the loss of older, now less acceptable pest management tools.
It called for more species-focused biological research so that new approaches could be developed and appropriately targeted.
There was a need for ongoing targeted efforts and investment to enable new approaches and technologies, and more trained local and central government staff who could translate and apply scientific research into new technology.
"Research into monitoring and surveillance technologies is also critical, because early detection of pests is essential to successful eradication, which is by far the best option," report co-author Dr Stephen Goldson said.
"There are new technologies that are increasingly being used to help with this effort, including the use of various attractants to uncover the presence and dispersal rates of invaders."
Kiwis could also help protect native land, aquatic environments and primary production from the increasing threat of pests, the report said.
"New Zealanders are very motivated when it comes to their natural environment and could probably play a much greater monitoring and surveillance role," report co-author Dr Stephen Goldson said.
"Obviously they need to be armed with information, and be involved early on."
The report comes as pest control efforts have been ramped up to protect 25 million native birds a year over the next five years, in what Conservation Minister Nick Smith has dubbed the "the battle for our birds".
The problem was urgent because the country was facing a large beech mast (bumper seeding), triggering a plague of an additional 30 million rats and tens of thousands of stoats, which would annihilate populations of endangered birds when the seeds germinate in spring.