Former Defence Force chief Tim Keating has faced a grilling about why the military took years to admit to possible civilian deaths in Afghanistan and how a key report proving official denials were wrong ended up "stuffed and buried" in a safe.

Meanwhile, the probe into Operation Burnham was abruptly suspended after finding a last-minute clue pointing to who may have had document locked away.

A Government inquiry is this week questioning current and former top NZDF brass about why the organisation called claims about the possibility of civilian casualties during the operation – an NZSAS-led counter-insurgency raid in August, 2010 – "unfounded" until 2014, and again in 2017, despite evidence existing to the contrary.

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.

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An International Security Assistance Force (ISAF) report in 2010 found that during the raid a gun-sight malfunction on a US Army helicopter led to rounds accidentally hitting two buildings and may have possibly killed villagers. It cleared New Zealand troops, who were on the ground.

The Burnham probe this week revealed a copy of the report reached the NZDF by September 2011, but was locked away in a safe and its findings not made public until 2014.

The military had erroneously from 2010 told Government ministers and public the report had ruled out civilian deaths, and now says it had not seen a full copy.

Lawyer for the inquest, Kristy McDonald, QC, described a key report as
Lawyer for the inquest, Kristy McDonald, QC, described a key report as "stuffed in a safe" and buried. Photo / Boris Jancic

In a lengthy interrogation by a lawyer for the inquiry, Kristy McDonald, QC, on Thursday, Keating defended the NZDF going back to calling the allegations "unfounded" after the release of Hit & Run, and again misrepresenting the conclusion of the ISAF report.

He said when the book had come out, his concern had been refuting suggestions New Zealand troops had committed war crimes, rather than previous claims.

"If somebody makes a claim that New Zealand Defence Force troops have targeted innocent women and children and murdered them, then what was in front of me and I had to get to the bottom of that," Keating said.

"That was what my imperative was… Not going back and looking at what we had said in the past."

Stephenson's lawyer, Davey Salmon, repeatedly rejected that Hit & Run at any point claimed the SAS had deliberately targeted women or murdered them.

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Keating said the allegations had serious potential to damage the mana and reputation of New Zealand troops and putting their lives at risk.

McDonald - at times seemingly frustrated with Keating's responses – asked if the NZDF's handling of the situation had been a "shambles".

"I think our processes … weren't coherent in giving the response we should have been able to give, in hindsight now," Keating said.

In the days following the press release, the former chief held a press conference saying civilian deaths may have occurred and launched an investigation into the claims in Hit & Run.

Keating was also questioned why the Defence Force had not made any statements after discovering the ISAF report contradicted its position in 2014.

He said because then Defence Minister Jonathan Coleman – incensed when he found out that the NZDF had been holding the document for years and giving out contradictory information – had made a statement, the Defence Force felt no need to.

Journalists Nicky Hager and Jon Stephenson, with lawyer Davey Salmon (middle), quickly scan the new evidence. Photo / Boris Jancic
Journalists Nicky Hager and Jon Stephenson, with lawyer Davey Salmon (middle), quickly scan the new evidence. Photo / Boris Jancic

The missing report

The inquiry was interrupted on Thursday after the discovery of a key piece of evidence pointing to how the ISAF report ended up in a safe in NZDF headquarters.

The probe earlier heard from retired colonel Michael Thompson the file had arrived in a bundle of classified documents that he placed in his safe on September 7, 2011.

It was also told the file was annotated and marked by someone when it was next seen in 2014, although no one has been able to say by whom.

Thompson said he could not recall who had given him the files to store and, from his own register, had no clues.

However, the inquiry's chairman, Sir Terence Arnold, on Thursday morning raised the possibility of a second register – asking the Defence Force to get a copy immediately.

A barrister assisting the inquiry, Lucila van Dam, said they had not been aware of the existence of the alternative log.

The inquiry was told it took about 15 minutes to find the file and heard the entry said the ISAF report had been checked in on September 1, 2011 by the director of special operations.

The director at the time was Colonel Jim Blackwell, according to van Dam. He is not appearing at the inquest this week.

The discovery of the new information on Thursday prompted a halt to the proceedings so new witnesses - including Blackwell - could be called to give evidence, and others hauled back to be re-examined.

Asked about Blackwell, Keating said he had a "high level of integrity I would not question".

Keating admitted processes for tracking documents at the time had not been up to scratch and said he had "fixed" the systems afterwards.

But he rejected a suggestion from McDonald that it had been "stuffed in a safe … and buried".

And during a heated session of questioning by Salmon, Keating, denied there had been a cover-up.

"It wasn't tidy, it was unprofessional, but it wasn't a conspiracy ... I take professional umbrage at that," Keating said.

He was, however, unable to say what investigation had been taken to figure out how the report ended up in the safe. He could also not say why his former chief of staff, Ross Smith - had not looked at the second register.

Smith earlier in the week said he had been unable to find the source of the ISAF report. McDonald suggested he may now be recalled.

The inquiry has heard the NZDF's incorrect understanding of the ISAF report came after its senior SAS officer in Afghanistan was allowed to read four lines of the report and misunderstood the actual conclusion that there may have been civilian deaths. That was then passed up the chain.

That was despite ISAF earlier issuing a press release to the contrary and another NZDF officer saying he believed civilians could have been killed.