The astonishing revelation came during the Assembly's Public Accounts committee's first public hearing into an audit of a tender related to the land swap, where Auditor-General Dr Maxine Cooper and audit staff gave evidence.

The audit prompting the committee's investigation found the government potentially relinquished up to $2.65 million in value for territory taxpayers to the CFMEU-linked club, through more "favourable" terms than the original tender allowed.

That deal saw the government pay the club $3.9 million for a block of land currently housing the union's office in Rosevear Place, Dickson, and $45,000 for a nearby block formerly housing the Downer club.

In return, the government sold the Dickson carpark, next to the Tradies Club, through a tender process to the club for $3.5 million, but settlement was delayed until a nearby development was completed.

While the audit did not find direct evidence of political involvement, Dr Cooper told the committee on Wednesday the investigation was hampered by a significant lack of paperwork detailing the negotiations over a two year period.

Chief Minister Andrew Barr has previously defended the deal, claiming it would help provide more social housing in Canberra, while Opposition Leader Alistair Coe has repeatedly slammed the deal as one that put the Labor Party's "fellow travellers" ahead of Canberra taxpayers.

Dr Cooper said there were 40 meetings in the year from December 2012 to December 2013.

The audit office's Brett Stanton told the committee that the office found "some emails" during that period, but there was little documentation about the actual meetings when the key details were decided.

Committee chairwoman, Liberal parliamentarian Vicki Dunne, said it had been suggested to the committee that "an officer left part way through [the talks], had all this [information] boxed up and set off". She asked Dr Cooper whether such action could breach the Territory Records Act.

Dr Cooper said that was a matter for the agency, but despite going back and forth to the current agency searching for such documents, the audit office "simply couldn't find some of the material people are saying exists".

"Now if it is in a box somewhere, that is a matter for the agency, in terms of what's happened to it," Dr Cooper said.

Dr Cooper said the audit office even had to "go hunting" to find a signed contract for the final deal reached and had to source "legal material to try and put the sequence of events together".

She said while there was some documentation there was "a lot lacking", when Labor parliamentarian Bec Cody interjected, saying there may have been "some lacking", to which Dr Cooper replied, saying "no, not some, I'd say a lot in this case".

"For instance, within the 40 meetings, you would expect some notes to help you understand why things were evolving through discussions, and as I said before, that's a fundamental issue around governance arrangements and integrity of a process," Dr Cooper said.

"As I said before, that's a fundamental issue around governance arrangements and integrity of a process."

Dr Cooper said she was unsure if the audit had also asked the club for records of the meetings, though the club had told auditors all the meetings were directly related to the land swap.

Asked by Mrs Dunne whether she would expect public servants to have a notebook for such meetings, Dr Cooper said there were "apparently some ... in this box of material".

"That's been put to us too that there might be notebooks somewhere but we couldn't find them and nor could the agency," she said.

Earlier during the hearing, Opposition Leader Alistair Coe asked about the potential motivation for completing the deal with the club, given talks went on so long, rather than cancel and re-issue a new tender to the market.

Dr Cooper said that would be "best put to the officials in charge at the time".

But said there seemed to have been a "culture of momentum" to close the deal with the club and it continued despite changes in economic development directorate senior staff during the protracted talks.

Ms Cody, a CFMEU member along with the other Labor MLA on the committee, Michael Pettersson, said there was a "relatively important point to make", that a former senior executive indicated there was "no political interference" in the deal.

But Dr Cooper said it was "a comment among many comments" and they sought clarification from the relevant minister, and the question for the audit team was "why are you telling us this now".

The audit shows the minister had responded that "at no time did the government signal a preference for the Tradies to be the successful tenderer to territory officials either formally or informally", despite such a perception being held by the former executive.

Mr Pettersson also asked Dr Cooper about the club disputing the $3.18 million valuation of the carpark block the club agree to buy, but Dr Cooper said if that had been the club's position during the negotiations, the club should have sought a new valuation.

In regards to the concessions, Dr Cooper said while a buyer could make an enormous amount of requests to adjust a tender, "the responsibility sits with the agency to have due diligence and probity of the highest regard".

The committee's inquiry continues.