A second senior military officer has claimed former Defence Minister Wayne Mapp was given a report showing the civilians may have died in a New Zealand-led mission in Afghanistan years before the Defence Force acknowledged the possibility.

But the head of the NZDF at the time cannot recall ever seeing the document.

A Government probe into Operation Burnham is this week questioning the Defence Force's former top brass about allegations of a "cover-up" and why it changed its story about whether civilians could have died during the mission.

The inquest 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.

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A report by the International Security Assistance Force (ISAF) in 2010 concluded that a gun-sight malfunction on a US helicopter led to rounds accidentally hitting two buildings during the operation – possibly killing villagers. New Zealand troops were cleared of wrongdoing.

But the NZDF until 2014 said the report had concluded "the allegations of civilian casualties were unfounded" and that those killed were insurgents.

The possibility of causalities was only acknowledged by Defence Minister Jonathan Coleman when he was handed a copy of the ISAF report in 2014 after media inquiries.

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 it was given to Coleman – who is said to have been furious about not having been told of the document's existence.

Several witnesses, including the Chief of Defence at the time, Tim Keating, told the inquiry they were shocked to learn the NZDF had the report in 2014, and there seemed to be no clue how it had arrived in New Zealand.

The last-minute discovery of a register pointed to retired colonel Jim Blackwell – the Director of Special Operations in 2011.

This week, Blackwell told the inquiry he received a copy of the 2011 report from his senior SAS officer in Afghanistan and had briefed Coleman's predecessor, Wayne Mapp - the Defence Minister from 2008 to late 2011 - in the Beehive soon after.

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On Tuesday, Retired capital Christopher Hoey – the director of co-ordination between the minister and the NZDF - on Wednesday told the inquiry a register showed he had received the report from Blackwell in September 2011.

"I am quite certain I would have given the documents to the minister straight away," he said.

Former Defence Minister Dr Wayne Mapp is due to give evidence on Friday. Photo / Pool
Former Defence Minister Dr Wayne Mapp is due to give evidence on Friday. Photo / Pool

Hoey said the document would have been considered important because of sensitivity around Afghanistan following the deaths of New Zealand soldiers and ahead of the 2011 election.

Asked why he had then not raised concerns that it contradicted the public story, Hoey replied:

"I would have skim-read the article, seen it was about an operation in Afghanistan and I would have put it on the minister's desk. I probably would not have sat down and read it in detail and analysed it against what had gone before."

He said the document given to Mapp had been shredded when he was replaced by Coleman in late 2011.

Blackwell earlier denied downplaying the significance of the report to the minister and said it was not up to him what was done with the information.

"I certainly didn't cover up anything," Blackwell 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."

Hoey said he did not have any details of the briefing to the minister.

The inquiry heard electronic records of the document had been deleted, something Blackwell said has he was surprised by.

He also said he had 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, saying the chief "needed to see" it.

But on Tuesday, Thompson repeatedly said he could not recall the conversation with Blackwell.

"There's the potential it could have happened but I don't recall this happening," Thompson said.

"It would stick in my mind for sure."

Jones told the inquiry he could not recall seeing or being briefed about the document while in the top job.

"I was not aware that there was a copy of the IAT report at HQ NZDF during my time as Chief of Defence Force," Jones said.

He said he also did not know if Mapp had ever been briefed.

Mapp is due to give evidence on Friday.

The Defence Force says its claims civilian deaths were "unfounded" were based on a misunderstanding of the ISAF 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.