The military's top brass will have to testify in open hearings over discrepancies in its account of whether it knew civilian casualties had occurred during the controversial 2010 raid by the NZSAS in Afghanistan.

The Inquiry into Operation Burnham issued an order for NZ Defence Force to appear during five days of public hearings and explain discrepancies which have emerged in its evidence.

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The decision to do so is remarkable given the Inquiry's previous insistence on avoiding collecting testimony in hearings which could lead to classified information being made public.

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The Inquiry was sparked by the book Hit & Run, which alleged six civilians were killed and 15 others wounded during the NZSAS raid in August 2010. The book alleged the raid was a revenge attack for the death of a New Zealand soldier, and claimed the civilian casualties were covered up.

NZDF consistently described claims of civilian casualties as "unfounded", although expanded its explanation after the publication of Hit & Run to say it had not ruled out the possibility.

The raid came to public attention in 2011, when then-defence minister Wayne Mapp was asked about it during a television interview. In response to direct questions, Mapp gave an assurance there were no civilian casualties.

His comments were in line with a briefing Mapp received in December 2010, which was offered by the Inquiry as an example of the discrepancies in NZDF's evidence.

The memorandum from the Inquiry said there was evidence from the immediate aftermath of the raid which showed NZDF was aware of the possibility of civilian casualties.

It included an email in which NZDF was told any civilian casualties had come about as a result of fire from United States' air support, which included an Apache helicopter gunship with a malfunctioning cannon.

Prime Minister Sir John Key visiting New Zealand soldiers in Bamiyan,, Afghanistan, in 2010. Photo / Supplied
Prime Minister Sir John Key visiting New Zealand soldiers in Bamiyan,, Afghanistan, in 2010. Photo / Supplied

However, in December 2010, Mapp was told "the allegations were baseless and categorically cleared the actions of the (NZSAS) and coalition air of all allegations".

The discrepancy was such the Inquiry said evidence about what NZDF knew, and what it then relayed to the Beehive, should be examined in public hearings.

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The Inquiry said NZDF "made firm statements publicly that no civilian casualties occurred" and went on to support ministers making similar statements.

"These actions were taken despite the repeated allegations of civilian casualties in the media and elsewhere from immediately after the Operation until the present.

"Given that the statements of NZDF and ministers were made publicly, the Inquiry considers that they should be explained publicly."

The matters the public hearings will cover include whether NZDF carried out its own inquiry into the possibility of civilian deaths, what steps it took to find out about civilian deaths and the basis for public statements made by ministers from 2010 onwards.

The Inquiry specifically pointed to statements made in 2011, 2014 and 2017 which saw subtle shifts in position by ministers.

The 2010 briefing which offered categorical assurances no civilians were killed was the focus of a Herald investigation last year.

The briefing, which was released by NZDF, showed Mapp and then-Prime Minister Sir John Key were told they were able to discuss the raid publicly if they wanted to do so. It also included the assurance no civilians had died.

NZDF responded saying a "phraseology" error was behind the assurance.

It said it appeared to stem from a NZSAS trooper reading the report of the investigation undertaken by the International Security Assistance Force and passing the gist of it back to New Zealand.

When received, the troopers summary was taken to be a direct quote from the report.

A spokesman for NZDF said at the time: "Understanding the sequence of these events, and how this came to transpire, will likely be an issue the forthcoming Government Inquiry will consider."

The new Inquiry memorandum: