New Zealand ranked far higher than its neighbour, with 20 per cent of SMEs and 27 per cent of larger firms bringing out "new-to-market" products.
Although the data was sourced from a 2007 OECD scorecard and drawn from surveys stretching back to 2004, researcher Luke Hendrickson defended the study.
Hendrickson said there was always a time lag in getting accurate and comparable data and said the report had the latest available information.
The Macdiarmid Institute's deputy director Shaun Hendy said although New Zealand may do better than Australia in some areas of innovation, the two countries both perform poorly when compared with other developed economies.
"We're actually quite similar when you stack us up together. Neither country is actually all that good at getting high-end technology products out there to the rest of the world," Hendy said.
"We're both dependant on commodities. In Australia's case it's largely minerals and in New Zealand's case it's dairy and meat products."
New Zealand's small size did give it some advantages over Australia, as it made it easier for research centres around the country to collaborate, he said.
However, he said there was little hope of closing the transtasman wage gap if companies do not spend more on research and development.
According to the latest figures from the OECD, New Zealand firms are spending 0.49 per cent of GDP on research, compared with Australian firms' 1.35 per cent.