However, it says the report was not fundamentally flawed and stands by its conclusions.
Pilot and father-of-two Bruce Andrews died when the Hughes 500 helicopter he was flying crashed in steep terrain in the Glade Burn near the Milford Track in December 2013. He was the only person on board.
The final CAA report of the incident was released in September, and Bruce Andrews’ brother, Robert Andrews, of Alexandra, labelled it "incompetent". He argued it contained inaccuracies, and that the process followed to produce it was "unprofessional".
The organisation then reviewed the investigation.
In an email to Mr Andrews in March, CAA deputy chief executive John Kay said "the investigation could have been better managed and conducted".
"There are weaknesses in the depth and clarity of the report (for example not citing evidence that could have strengthened the conclusions). And as you have pointed out, the peer review process was not as effective as it should have been, and led to an excessive number of ‘versions’, some of which contained factual errors.
"I will be tasking the appropriate staff of the CAA to make changes to the processes and protocols followed. Your observations and comments in this regard have been valuable to the CAA, and I am grateful you raised them with us."
The CAA was not able to clarify yesterday how processes and protocols would change as Mr Kay was on leave.
In the email, Mr Kay continued: "However, I cannot find any evidence to suggest that the investigation team lied or were in any way deliberately and intentionally misleading."
The investigation was conducted with the "right intentions", he said.
"I have concluded that the investigation itself, while not perfect, is not fundamentally flawed and has reached reasonable conclusions. I appreciate that those conclusions and findings are challenging for you and the other members of the pilot’s family.
"I apologise to you and the other family members for the distress caused by the prolonged nature of the investigation and reporting process."
Robert Andrews said he was "not happy" with the response.
"They don’t agree with our version of events, essentially."
The family was concerned the initial report moved away from a medical cause for the incident to one placing the blame on flying in adverse weather.
The review of the investigation concluded a medical event could not be ruled out, but it could not be cited as the cause of the accident.
Mr Andrews said there was also no evidence his brother flew into cloud, as the report suggested.
He also took issue with the report mentioning his brother flying under 500ft, which he was not allowed to do under aviation rules.
The CAA provided no evidence of this, he said.
The revised report was "pretty much the same" as the original version, he said.
"Well, I’m not surprised. I still think they’re wrong in that they still have no evidence he flew into cloud. They are sticking to the same old line.
"It’s a waste of time. They don’t want to talk to us."
Civil Aviation Authority communications manager Mike Richards said the family was "most welcome" to engage further with the organisation.
The case is still before the coroner.
