The plane crashed during take-off on September 4, 2010, the same day as the first Christchurch earthquake.
Today's report found problems with the "resourcing of the investigation, the management of evidence at the accident site and the analysis of the evidence".
"The reviewer found that resourcing at the accident site was not adequate, that procedures for the control and handling of evidence, and file noting, on site could be improved and that while the analysis undertaken was generally good, further testing and analysis could have been undertaken."
The reviewer found "gaps" and "weaknesses" in the commission's resourcing and procedures, although said the investigation took place under strained circumstances.
The only available investigator on the day had to travel from Christchurch, where his house and family had been affected by the quake.
The commission's original report was released in May 2012, but a year later a coroner's report found the weight of the aircraft and its balance combined with unidentified factors were to blame.
Soon after the crash and at the direction of the commission, parts of the plane, including the control stick, were buried in a paddock at the end of the Fox Glacier airstrip.
Four overseas backpackers and five Skydive NZ staff members were killed in the crash.
TAIC chief commissioner Helen Cull QC said the commission would not apologise to families of the victims.
"Everyone was trying to do their best to see if they could be definitive about the way the plane pitched up."
She said it should be clear "how seriously" TAIC took the investigation review.
"Our actions speak louder than words."
The commission said it secured $1.2 million in new funding from the Ministry of Transport for extra investigators.
It took some 27 hours for a Christchurch-based investigator to reach the crash site.
But TAIC chief investigator Tim Burfoot and Ms Cull today told a press conference the new investigators would be based in Wellington, as the cost of having regional offices was too high.
Mr Burfoot said it should be remembered that several hours passed before the commission was notified of the crash.
Some of the crash victims' relatives were outspoken in their criticism of the commission's investigation.
Ms Cull and Mr Burfoot said today TAIC had been in frequent contact with the family.
Ms Cull said she did not accept a description of the investigation as "lacklustre" and insisted the Commission did what it could with the resources it had at the time.
"Obviously with the benefit of the review, some things could have been done differently... The senior investigator, the only one available at that time and on that day, went despite the personal damage that had been done both to his home and the upset to his family."
Nobody at the commission faced disciplinary action.
"Why would we? He's done a very good job, under the circumstances," Mr Burfoot said, referring to the senior investigator.
Another investigator was overseas at the time, compounding what Ms Cull called a "peculiar" set of circumstances that day.
The accident was New Zealand's worst aviation disaster in 17 years.
Those who died in the accident were:
Four tourists:
Patrick Byrne, 26, from Ireland
Glenn Bourke, 18, from Australia
Brad Coker, 24, from England
Annita Kirsten, 23, from Germany
Four Skydive NZ dive masters:
Adam Bennett, 47
Christopher McDonald, 62
Rod Miller, 55
Michael Suter, 32
And their pilot, Chaminda Senadhira, 33, known as Chami.
