In its submission to a review of the country's existing quarantine arrangements, NFF president, David Crombie, said a breakdown in quarantine as seen with horse flu had triggered a lack of confidence in the system which needed to be addressed by the Government.

Mr Crombie said technical capacity in the system has been reducing over time, particularly within State Departments of Primary Industry and the CSIRO, which had put pressure on the nation's border protection.

"All levels of government must ensure they have the resources and expertise to meet the programs they are charged with," Mr Crombie said.

"The NFF is calling for an injection of resources and targeted strategies to ensure these deficiencies are rectified, along with long-term safeguards so they don’t reoccur."

While NFF has previously been criticised by some farmer organisations for not going hard enough on quarantine issues because of the potential conflict it might have with its free-trade policies, Mr Crombie said transparent, science-based quarantine and biosecurity that protect Australia's environment, biodiversity and agricultural systems "assume even greater importance in this modern era of global movement of people, animals and goods".

"Our quarantine and biosecurity effort simply hasn't kept pace with modern demands and will be under increasing pressure," Mr Crombie said.

"NFF believes we can improve our quarantine system by forging more effective links between the various government agencies, at both the Commonwealth and State/Territory levels, as well as closer consultative arrangements with industry.

"The 2007 EI outbreak highlighted breakdowns and painfully demonstrated how damaging and resource intensive an incursion can be. We have to get it right."

The Federal Government has still not released the report into last year's EI outbreak, but Minister for Agriculture, Tony Burke, said the government would do so once its response to the report was finalised.