The air force has, until now, had internal rules about dangerous goods but no formal requirement to comply with CAA rules when transporting dangerous goods on civilian aircraft.
The report also recommended a Memorandum of Understanding be established between the CAA and the NZDF to improve the availability of technical advice, guidance and incident reporting between agencies.
"The CAA's safety investigation unit, conducted an investigation into the areas found to be warranting further scrutiny by the interim report," CAA general manager of policy, systems and interventions of civil aviation John Kay said today.
"In particular, these focused on the civilian elements of the incident that were not covered by the RNZAF's own investigation and procedures rules applying to the NZDF when consigning dangerous goods on civilian aircraft and the reporting procedures between the NZDF, and civilian organisations to support this."
The Air Force "acknowledged" the report, saying it would be working with the CAA to implement its recommendations.
"As noted when the CAA released its Interim Report in October 2012, the RNZAF reviewed its procedures to ensure it meets all civil and military regulatory obligations and implemented the necessary reforms in response to the dangerous goods incident in 2009," Chief of Air Force, Air Vice-Marshal Peter Stockwell said in a statement.
"All recommendations from the 2009 RNZAF Court of Inquiry into this incident have now been actioned."