In September, the Opposition blocked a Government decision to remove a 40 per cent subsidy for quarantine inspections and reforms to the export system, arguing it would cost rural jobs, particularly in the agricultural and food processing sectors.

The Government policy was aimed at full cost recovery for its export and quarantine services.

Mr Burke said the decision today would enable the changes to proceed, but under a different time frame and funding package.

"This is the largest reform in a generation and has the overwhelming support of the red meat, dairy, grain, fish, horticulture and live export industry sectors," Mr Burke said.

"This program will cut red tape by updating IT systems helping to improve market access.

"The reform program funds improvements to make export certification processes more effective and efficient, helping us respond to ever-increasing scrutiny from our export markets."

Under the new deal announced today, the 40pc rebate will continue for another two years, during which time exporters will be assisted in adjusting to the new rules.

The new package includes:

· $85.3m to reintroduce the 40pc rebate for two years;

· $16.1m to implement regulatory and export supply chain reforms;

· $26m for redundancies to now be paid for by the Government;

· Accumulated industry debts to be wiped;

· Small meat processors will have their registration charges dropped from $50,000 to $17,800; and

· Regular audits to ensure industry is only paying for legitimate costs.

Opposition agriculture spokesman John Cobb said the current economic environment and the high value of the Aussie dollar had resulted in many agricultural exporters doing it tough at the moment.

"Given the extremely tight margins, the increased AQIS fees were potentially the knock out blow for many companies," Mr Cobb said.

"The Minister’s decision to put policy ahead of politics is good news for companies like the Mildura Fruit Company which earlier this month said the removal of the 40pc rebate by the Rudd Government had made exporting fruit to some countries ‘uncommercial’.

"The Coalition had always made it clear that reform of the AQIS Export Certification program was our main priority. However, we were not prepared to see companies busted by the full fee increases."