The commission found there was lack of data and research from which to conclude flight training safety was in decline, and anecdotes of system-wide issues were unsupported by the evidence.
That was despite figures which showed an increase in flight training fatalities in the past decade compared with the previous decade.
There were 16 fatalities from 10 training incidents between 2000 and 2011, compared with four fatalities from four training incidents between 1988 and 1999.
Over the past decade, the number of training incidents reported has steadily increased, from 80 to 200 per 100,000 flying hours.
But the commission found that may reflect an increase in flight training activity and an improvement in incident reporting culture, rather than a decline in the overall safety of the training industry.
Mid-air collisions accounted for only 2 per cent of all flight training incidents in the last decade, but a third of the fatalities.
The commission found fatality rates for training incidents were comparable to those in Australia and the United States.
It also noted data and research showed flight training was generally one of the safest forms of flying activity.
Chief commissioner John Marshall QC said a recurring theme throughout the inquiry was the lack of data and research.
That meant the commission was unable to confirm or dismiss some of the issues which had been raised in submissions.
"Better data collection and analysis could confirm any existing issues or allow them to be found in the future - and this work is the job of the Civil Aviation Authority."
The commission recommended the CAA review its data systems and processes, do more quantitative safety research, and improve instructor demographics and performance data - recommendations which the authority had accepted.
It also recommended the CAA give priority to its work to tighten pilot licensing requirements and ensure the same standards were required from all types of flying training providers.
The commission also made recommendations about pilot communications, following its investigation into the Feilding mid-air crash.
It found the pilots of both aircraft were making the required radio calls about their locations and flight paths, but neither the instructor nor the two students appeared to have recognised their planes were on course to collide soon enough.
"The surviving pilot certainly did not see the other aeroplane before the collision, and it was not possible to determine if the flying instructor and the student in the other aeroplane saw his plane before the collision," Mr Marshall said.
"So the pilots of both aircraft appear to have either not heard - or to have heard and not comprehended - the importance of the radio calls of other aircraft.''
The commission said the collision - as well as a fatal mid-air collision over Paraparaumu in 2008 and a near-collision over New Plymouth in 2010 - all involved instructors who should have been capable of recognising the potential for a mid-air collision and taking action.
"It appears in these cases the instructors might have been focussing more on instructing or examining the student pilots and less on ensuring the safety of their aircraft," Mr Marshall said.
It recommended the CAA inform flight instructors that their first responsibility is the safety of the aircraft, ahead of instructing student pilots.
It also reminded instructors to ensure students are able to listen for, see and avoid other aircraft before being allowed to fly solo.
The commission said the CAA should educate pilots, particularly those involved in training, about the importance of making clear and concise radio transmissions to warn of location and flight paths.
The CAA said it believed it was already doing enough in these areas, but the commission said it had sought more information before accepting that.
