State Services Minister Jonathan Coleman - also Defence Minister - ordered the inquiries after a Herald investigation identified missed warnings and safety failings which led to the three air force staff dying in the 2010 crash.
The Herald inquiry also revealed an internal air force report had raised concerns about safety across the entire air force.
The State Services Commission was able to access those documents - and has ordered extensive change.
Chief of Air Force Air Vice-Marshal Peter Stockwell has avoided interviews on the issue. In a statement he greeted the report as an endorsement of the air force's approach. But he also said: "We accept all ... recommendations and we will ensure that these are implemented."
The commission report said a new governance structure which would better identify safety risks was needed. It would help find potential problems when decisions including "resource allocation" impacted on "operational safety".
The review found the new structure would be "critical" for the Chief of Air Force to demonstrate all possible was being done to protect the 3300 air force personnel. It also found 85 per cent of the 78 safety recommendations made following the crash had been put in place.
The number had risen from 15 per cent in March - almost two years after the accident and before the Herald began investigating the accident.
The report found the air force had closed recommendations which had not been carried out - ground proximity warning systems had not been fitted to NZDF aircraft, locator beacons for air crew and aircraft had not been sourced and there were still no cockpit voice recorders installed. The air force had found it was not possible to fit the equipment to all aircraft so was deciding which would get the new equipment.
The review also highlighted problems in critical auditing, command and oversight bodies which work to manage workloads and review safety. It found the groups, 485 Wing and 488 Wing, had a number of vacancies and staff normally working there had been posted to other NZDF projects.
The report recommended the air force adopt management and safety systems used in Australian, British and commercial carriers like Air NZ.
The current system, it found, was not suited for carrying out military air operations or dealing with organisational change. Among problems were "short term trade-offs" where training was sacrificed to deal with jobs which needed doing.
The air force's "Operating Airworthiness Regulator" - who reports direct to the Chief of Air Force - drew parallels between "the current state of RNZAF airworthiness" and an inquiry into the crash of an RAF Nimrod in Afghanistan which killed 14 people.
It identified safety issues known in the air force as the "dirty dozen", which included bad systems, overworked staff, and cuts in funding and staff.
The second report recommended health and safety inspectors with military experience be hired.
It also identified a string of gaps in parts of the military covered by workplace safety agencies.
Mr Coleman did not respond to calls for an interview. In a statement he said: "The RNZAF is taking every step it can take to ensure it never happens again."
