Mystery surrounds the disappearance of key documents relating to negotiations over an alleged deal between construction giant John Holland and the Australian Workers' Union that began when Opposition Leader Bill Shorten was in charge.

A 7.30 investigation has prompted the trade union royal commission to say it will treat seriously any allegation that documents relevant to its inquiries have been improperly destroyed.

The commission also says any new information about the location of the documents will be investigated.

It has heard the documents, including red notebooks and copies of emails, relate to negotiations between the Thiess John Holland consortium, which built Melbourne's $2.5 billion Eastlink toll road, and Mr Shorten when he led the Australian Workers Union (AWU).

It heard the documents discussed Mr Shorten's involvement in the negotiations that resulted in an agreement that delivered $100 million in worker productivity savings in exchange for the consortium paying a salary for an AWU organiser at a total cost of $300,000.

Do you know more about this story? Email 7.30syd@your.abc.net.au

Mr Shorten has always maintained he did not strike such a deal.

"I did not strike any agreement of the nature you are raising — full stop," Mr Shorten told reporters at a press conference last week, reiterating his earlier statements at the royal commission.

7.30 has been told the notebooks were not kept at John Holland, but went off-site to the Recall secure storage facility in Sydney's Alexandria, and were labelled with dates and marked by a personal assistant to a former John Holland executive not to be destroyed for seven years — that was five years ago.

The program has learned the personal assistant also scanned key pages of the notebooks as a back-up and then saved them to the company's internal server.

But in an exchange of emails tendered to the royal commission, John Holland has said that none of the documents can be found.

Efforts of former John Holland executive to protect evidence

The former executive, Stephen Sasse, is a self-confessed assiduous record keeper who was at pains to protect material which might be litigious in the future.

Former John Holland executive Stephen Sasse says he went to great lengths to protect the relevant documents. ( ABC 7.30 )

He has never spoken publicly outside the royal commission, but 7.30 tracked Mr Sasse down as he was about to board a plane.

When asked if he found it curious that John Holland had said the notebooks could not be found, Mr Sasse replied: "I'm surprised, yes."

In correspondence to the royal commission's lawyers, John Holland said it no longer had Mr Sasse's computer and the C: drive disk had been removed and destroyed.

But Mr Sasse said he saved relevant emails with other consortium executives about his discussions with Mr Shorten to an internal company hard drive.

"The concept that the documents that have been looked for by the royal commission are being stored on the C: drive of a laptop is verging on the ludicrous," Mr Sasse told 7.30.

'Someone, somewhere, will want this'

Mr Sasse confirmed that the company used Recall, which prides itself on its ability to securely maintain documents.

He also told the royal commission in evidence last Monday: "When I left John Holland, I handed both my notebooks and my paper diaries to my PA with very clear instructions to put them somewhere where they could be found again and made a comment 'someone, somewhere, will want this'."

That someone turned out to be trade union royal commissioner, Dyson Heydon, who wrote on June 29 to ask for documents which would include the notebooks.

This was 11 days after Fairfax Media splashed with a story which contained key elements of the alleged deal between the consortium and Mr Shorten — so the company was aware that the commission could come knocking.

Mr Sasse was so determined to help find the documents; royal commission records show that earlier this month, he personally wrote to John Holland, explaining where it might find the material.

John Holland's response was short and curt: "You will no doubt understand that John Holland has already provided to the commission copies of the relevant documents we could locate ... Any such documents would have included the documents you refer to in your letter if they were located."

Penalties if documents found to be concealed

While it is not known what happened to Mr Sasse's documents, barrister Gregory Lyon QC has pointed out the possible ramifications.

"I'll preface my remarks by saying that I'm not going to comment on the evidence or the issues before the royal commission at the moment," Dr Lyon said.

"But under the Royal Commissions Act 1902 there's a penalty provision under section 6K which provides if a document is concealed, mutilated, destroyed or otherwise made indecipherable then the person responsible for that can face up to two years' imprisonment or a fine of up to $10,000."

Those provisions relate not just to material the royal commission has already asked for, but material which could reasonably be expected it might ask for.

7.30 sent John Holland a very detailed list of questions about the whereabouts of the documents, what its document retention policies were and even if it was simply a mistake — the company declined to comment.

Covering up negotiations of organiser deal

Mr Sasse told the royal commission that Mr Shorten proposed the $300,000 payment. He said it comprised of a salary for an organiser of $75,000 per year plus a car.

The negotiations between Mr Sasse and Mr Shorten have been particularly explosive because Mr Sasse's successor in the job, Julian Rzesnowiecki, gave evidence to the commission that Mr Shorten's successor, Cesar Melham, created a series of sham invoices to cover up the deal that Mr Shorten had commenced.

"The main purpose was to, you know, disguise the fact that we were funding an organiser," Mr Rzesnowiecki told the royal commission.

Mr Rzesnowiecki revealed a diary note from December 2004 in which he said Mr Shorten was present during preliminary negotiations about the organiser deal.

Lawyers for Mr Shorten have attempted to discredit Mr Sasse — who gave an address to a right-wing think tank last year about the extent of union influence on the industrial landscape.

But Mr Sasse maintains that is immaterial to his allegations in the royal commission.

When asked if he was "just trying to bring Mr Shorten down" Mr Sasse replied: "I have no interest in that whatsoever."

Editor's note (21/10/15): This story has been amended to make clear that the allegation is that negotiations on a secret deal between John Holland and the AWU started while Bill Shorten was AWU National Secretary, not that the alleged deal was completed while he led the union.