Crucial evidence naming the SAS commander who handled a report confirming possible civilian casualties has suddenly emerged to upset the Operation Burnham inquiry.

The evidence, a register which identifies when the report was placed in a safe in the office of the chief of defence, was obtained in 15 minutes by a Defence Force staffer, despite it being mistakenly or intentionally overlooked for years.

This throws into question the evidence of numerous SAS commanders, causing the inquiry to end a week-long hearing early to prepare for re-examination of witnesses. 

The development comes as former Chief of Defence Force Tim Keating argued with lawyers at a hearing on Thursday, answering questions with questions and routinely saying, "I don't understand the question," and, "I'm not being cute here".

The inquiry was this week inspecting claims of a Defence Force cover up, claimed by the book Hit & Run which contained allegations that six civilians were killed during a 2010 SAS-led raid in Afghanistan.

Brigadier Chris Parsons told the inquiry earlier this week he wrongly relayed a fleeting glance of the report's findings to his superiors in 2010, leading the military to advise the Defence Minister allegations of civilian deaths were "baseless".

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This denial only changed in 2014, when the International Security Assistance Force (ISAF) report was accidentally found in a safe in Wellington, confirming the possibility civilians were killed by errant shots fired by a US Apache helicopter.

Of the 11 senior military officers who have so far appeared before the inquiry, all have said they had no idea how the report came into Defence Force hands.

Keating and chief of staff Commodore Ross Smith were tasked with investigating this by Defence Minister Jonathan Coleman in 2014, and apparently verbally briefed the minister that this was not successful.

Keating said the overlooked report was a failure of administrative systems, which he addressed.

"What I believe is the document arrived in a bundle, into a safe, and it remained dormant," he said on Wednesday.

But Keating was able to describe how classified documents were registered in his former office, leading inquiry chair Sir Terence Arnold to ask for the evidence. 

Somehow this register had gone unchecked for five years until Thursday, and wasn't provided by the Defence Force for the inquiry which has now been running for nearly 18 months.

The lawyer for the Defence Force, Lucila van Dam, told the inquiry the existence of a register had not been made apparent in her investigation for evidence.

The register confirmed the director of special operations in September 2011, Jim Blackwell, had signed the report into the office. 

Van Dam said Blackwell had said he did not remember seeing the report. But he did not appear on the list of witnesses chosen by the Defence Force. 

Keating confirmed he knew Blackwell well, as they had served together in the SAS. But he did not know why Blackwell was not appearing. 

Inquiry lawyers asked he present as a witness at a future hearing.

Lawyer for the Hit & Run authors, Davey Salmon, asked Keating why it appeared there was "multiple former and current SAS operatives, who know each other well, in key times in this process".

"Do you agree … This looks like there was a degree of co-ordination between multiple members of your office to conceal the true position from the minister and the public?"

Keating said: "It wasn't tidy and it wasn't professional, but it wasn't a conspiracy."