A new report proposes the formation of a new national biosecurity authority which would bring together the functions of AQIS, Biosecurity Australia and parts of the Department of Agriculture, Fisheries and Forestry, at an annual cost of $A260 million.
The report from an expert panel chaired by Roger Beale, entitled "One Biosecurity: A Working Partnership", says the growing threats of climate change, globalisation and agri-terrorism mean Australia needs to overhaul its biosecurity system.
The report makes 84 recommendations, representing the biggest reforms to the country's biosecurity system in more than a century.
It held 170 meetings with domestic and international stakeholders and received more than 200 submissions.
Federal Agriculture Minister Tony Burke said the government had accepted all 84 recommendations in-principle, but more consultation was needed on how to implement the findings and fund the reforms.
Interim administrative arrangements will take effect from July next year.
Burke says the government is determined to recognise the risks and act to ensure Australia is better prepared.
"This includes building a 21st century biosecurity system to meet 21st century challenges.
"We are processing record numbers of visitors and sea cargo and face greater risks from climate change and the threat of agri-terrorism.
"The equine influenza outbreak last year was a stark reminder of the devastating effect of an exotic disease on people's lives and jobs."
The report was released just seven days before Australia is formally recognised as free from equine influenza under international guidelines set by the World Organisation for Animal Health (OIE).
Australia's quarantine service was blamed for the escape of equine flu from its Eastern Creek quarantine station, with an earlier inquiry identifying serious lapses in biosecurity.