The extraordinary and historic nature of the inquiry into a controversial NZSAS raid was laid bare amidst concerns over the release of classified and secret information.

Those secrets meant it was likely the inquiry would be "one of the most complex in New Zealand's history", said Kristy McDonald QC, whose role was to help dig out and report the truth behind the raid commonly known as Operation Burnham.

"While other countries have undertaken public inquiries into the activities of their armed forces while in service overseas, this is the first in New Zealand to do so as far as we are aware."

McDonald's words gave context to what was expected to be one of the few open and public hearings to be held by the inquiry.

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The two-day hearing was intended to set out a process by which the inquiry would operate, including how much information would be made public and the reasons for secrecy.

Its genesis was the book Hit & Run, which brought the most serious allegations ever to be aimed at the elite NZSAS.

The book, by authors Nicky Hager and Jon Stephenson, was published 18 months ago and alleged war crimes, the death of six civilians and wounding of 15 others during a "revenge" raid in Afghanistan on August 22, 2010.

The NZ Defence Force has utterly rejected the premise, saying the NZSAS acted with honour and integrity in an operation which saw nine insurgents killed.

There was no inquiry until there was a new Government, when Attorney General David Parker said one must take place because of "the need for the public to have confidence in the NZDF".

It began in a basement courtroom in the High Court at Wellington.

The intent was to get to the truth, said Sir Terence Arnold QC, former Supreme Court judge, introducing himself and former Prime Minister Sir Geoffrey Palmer as the chairmen who would consider and weigh evidence in the inquiry.

McDonald explained the search for the truth amidst classified documents and the secretive NZSAS was fraught.

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Careless production of classified information could pose a real and significant damage to the interests of New Zealand and its citizens, she said.

Yet, said McDonald, an inquiry which was insufficiently open threatened the ability to engage public trust.

The threat was not just direct but required considerations on the impact of releasing information which belonged to other governments.

She said New Zealand relied heavily on intelligence from foreign governments and some of this was information needed for the inquiry.

If information from other countries was disclosed it would likely breach agreements, which in turn could lead to a reduction in sharing and - as a result - damage the interests of New Zealand.

"The inquiry ought not place itself in the position of damaging the interests of New Zealand, or the public, by its conduct."

The public gallery was about two-thirds filled, outnumbered by those in the business end of the courtroom.

Along with the knighted chairmen and McDonald were those with a specific interest in what had happened.

On one side of the equation was Hager, representing himself, and lawyers representing Stephenson. Deborah Manning, who famously represented asylum seeker Ahmed Zaoui, was there for the Afghan villagers.

They have sought greater openness while also seeking protection for the identities of journalistic sources and the villagers.

On the other, there were lawyers for the Crown - there for diplomatic and intelligence interests - and separate lawyers for the NZ Defence Force.

The intelligence agencies, NZDF and the supporting government establishment have pushed for almost complete secrecy on the basis of protecting classified information associated with the raid.

There were also those whose interest fell neither one way or the other. There was Bruce Gray QC, who was representing former Defence Minister Wayne Mapp - a pivotal player at the time later revealed as a source for the book who held nagging doubts over what had occurred.

And there was Bell Gully partner Alan Ringwood, who was there for the nation's media, with submissions pushing for as much openness as possible.

The opening of the inquiry revealed it was misnamed. Its official title is Inquiry into Operation Burnham, yet submissions revealed there never was an "operation" called Burnham.

Instead, there was an "Objective Burnham" - one specific individual who was the target of the NZSAS on the night of August 22 in 2010.

There were two other objectives - in total, three men had been identified as the insurgents responsible for attacks on New Zealand and other coalition forces.