A former top military commander has denied covering up a report that concluded civilians may have been killed during a New Zealand-led raid in Afghanistan years before the Defence Force admitted to the possibility, and says he told the Minister of Defence about it.

A Government inquiry into Operation Burnham is this week questioning the senior officials about shifting NZDF accounts of the raid.

The inquiry was spurred by the 2017 book Hit & Run, in which journalists Nicky Hager and Jon Stephenson alleged six civilians were killed and 15 others wounded during the NZSAS-led raid in August 2010.

The NZDF publicly described the claims of possible civilian deaths as unfounded until 2014, but it later came to light an International Security Assistance Force (ISAF) report in 2010 had found a gun-sight malfunction on a United States Army helicopter led to rounds accidentally hitting two buildings during the operation – possibly killing villagers.

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It cleared New Zealand troops of wrongdoing.

The inquiry last month heard that report had been given to the Defence Force in 2011 but was locked in a safe at its headquarters for three years before its conclusions were made public.

A number of witnesses earlier told the probe they had no idea how the document ended up there and that then Defence Minister Jonathan Coleman was furious when he found out about its existence in 2014. He went on to correct the public record.

On Monday, retired colonel Jim Blackwell – the Director of Special Operations in 2011 – said he had requested the ISAF report from senior officers in Afghanistan and eventually received an electronic copy on September 1, 2011.

Blackwell said he then briefed Coleman's predecessor, Wayne Mapp - the Defence Minister from 2008 to late 2011 - in the Beehive.

Former Defence Minister Dr Wayne Mapp at an earlier hearing.
Former Defence Minister Dr Wayne Mapp at an earlier hearing.

"Although I do not recall the date or the logistics of the briefings, I do recall explaining to the minister that the IAT report did not provide evidence that civilians were killed but that it did conclude there was the possibility of uninvited civilian casualties," Blackwell said.

"The minister was very familiar with the document when I briefed him."

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Lawyer for the inquiry, Kristy MacDonald, QC, pressed Blackwell on whether he had downplayed the report or its significance in the briefing to the Minister.

"I want to know whether you or Dr Mapp made a decision to cover this up and play it down for the public," Kristy asked.

Blackwell said he had no reason to talk the report down, given it exonerated his troops.

"I certainly didn't cover up anything," he said.

"I don't wish to make any remarks on what Dr Mapp may or may not have done … It's not for me to do that. It's inappropriate and unfair to do so."

Blackwell said the report had arrived during a busy period for the NZDF in Afghanistan and it would have just been one of a number of operations raised with the minister.

The inquiry heard no digital record of the report arriving appeared to remain.

"I'm as amazed by this as you are," Blackwell said.

Mapp, who previously testified at the inquiry, has been recalled among other witnesses to give evidence about the report on Friday.

Blackwell said he had also passed a copy of the ISAF report to the office of then Chief of Defence Rhys Jones, through his deputy chief of staff, Mike Thompson - and briefed the chief on it at some point.

Retired colonel Thompson earlier told the hearing the file had arrived as a bundle of classified documents and he placed in his safe on September 7, 2011.

"I have never read the bundle … I believe someone must have asked me to put it in the safe; in other words, my safe was simply used as a classified repository. I cannot recall who that person may have been," Thompson said.

"I put the briefing pack in the safe, recorded it in, and that was it."

He has been recalled to give further evidence this week, as has Jones - who earlier told the inquiry he never saw the report either.

The Defence Force says its claims civilian deaths were "unfounded" were based on a misunderstanding of the report by New Zealand's top SAS officer in Afghanistan in 2010.

The NZDF's then Senior National Officer, Brigadier Christopher Parsons, told the probe he had only been allowed to see one paragraph of the report in September, 2010, and as a result incorrectly reported back no civilians had died.

That formed the basis of incorrect briefings to ministers and the Prime Minister until 2014 and public statements about what ISAF had found, the probe has heard.

The inquiry this week announced it would be extending its deadline out to March next year. This week's hearing is expected to be the last open to the public.