It found more than 13 failures for every 1000 positive cases going through a facility in New Zealand versus 4.1 failures per 1000 in Australia - more than a three-fold difference in risk.
The failure rate per 100,000 travellers was 7.8 in New Zealand compared to 5.5 in Australia.
The report said one reason for New Zealand's significantly higher failure risk is it had a "lower-quality approach".
"The significantly higher failure risk per 1000 SARS-CoV-2 positive cases transiting quarantine in New Zealand versus Australia could reflect a lower quality approach in the former, with perhaps some of the difference due to greater detection in New Zealand from more border worker testing over a longer period."
There were a total of 24 failures.
"In Australia, 14 failures were identified, one causing over 800 deaths (Victoria's second wave) and eight out of the 14 resulting in lockdowns," the report said.
"In New Zealand, there were ten failures, with one causing an outbreak with three deaths, and also a lockdown."
Failure risks in both countries could increase as infection rates increased overseas because of new virus variants, it said.
However, the vaccination rollout would offset some of this, it said.
"Approximately 55 percent of quarantine system failures could likely have been prevented with the full vaccination of frontline border workers, for 70 percent effectiveness at preventing transmission."
The authors suggested measures such as reducing the number of arrivals from high-risk countries, expanding pre-departure testing and alternatives to hotel-based quarantine.
Some of the figures in this story have been updated based on the most recent version of the report, with the authors finding an extra two quarantine failures in facilities in Australia.