Opposition Leader Bill Shorten has emphatically rejected accusations of a conflict of interest after emerging from two days of questioning at the royal commission into union corruption in Sydney.

Mr Shorten has been interrogated about payments the Australian Workers Union (AWU) received from various companies while he was its state and national secretary.

During the hearing the Opposition Leader fended off suggestions those payments created conflicts of interest as the union negotiated wages and conditions for workers employed by those companies, which included Thiess John Holland and glassmaker ACI.

As he left the inquiry Mr Shorten reiterated his position.

"There was no evidence demonstrated of any conflict," he said.

"The truth of the matter is that every day I was a union rep I was standing up for our members.

"Of course where we could, we would cooperate with employers for the best interests of our workers. No conflict of interest whatsoever."

AWU invoiced Thiess for more than $300k

The inquiries on Thursday began with the focus on invoices issued from early 2005 by the AWU to construction firm Thiess John Holland totalling more than $300,000.

Some of the money was for "research work done on back strain in the civil construction industry", according to the invoices, although Mr Stoljar said records of that research had been sought from the AWU but "nothing has been produced".

Mr Shorten said the fact no records were received "just suggests to me that the AWU can't find the research".

"Is this a bogus invoicing claim for work that was never done?" Mr Stoljar asked.

Mr Shorten replied: "I would never be party to issuing any bogus invoices, full stop."

In a heated exchange, Mr Stoljar asked several times whether Mr Shorten accepted that "a separate side deal" - the $300,000 worth of payments - with Thiess John Holland would represent "a serious conflict of interest" for a union trying seek the best deal for its members.

Mr Shorten called that question "hypothetical".

"That is not what the AWU in my time was doing," he said.

Mr Shorten was also quizzed about deals between the AWU and glassmaker ACI, which evidence showed paid the union hundreds of thousands of dollars over several years, some of which was apparently used for "paid education".

"Isn't it the position that the paid education income simply went into the consolidated revenue ... of the union," Mr Stoljar asked.

Mr Shorten rejected that, and said he was "most committed to raising whatever we could for education."

He also defended the union's agreements with Chiquita Mushrooms, which ran farms in Victoria, and Victorian building company Winslow Constructors.

Shorten accused of being 'non-responsive' in hearing

Earlier the head of the royal commission warned that Mr Shorten's "extraneous" answers to questions could have put his own credibility as a witness in jeopardy.

Sorry, this video has expired Shorten warned over 'credibility' at trade union royal commission

Commissioner Dyson Heydon QC took a moment to criticise Mr Shorten for the pace at which the hearing was proceeding, saying a lot of Mr Shorten's answers were "non-responsive".

"What you have been saying, in what I am calling non-responsive parts, may well be true, may well be relevant, [and] parts of it are very interesting," Mr Heydon told Mr Shorten.

"You, if I can be frank about it, have been criticised in the newspapers in the last few weeks and I think it is generally believed that you have come here in the hope that you will be able to rebut that criticism.

"I am not very troubled about that.

"What I am concerned about more is your credibility as a witness ... and perhaps your self-interest as a witness as well."

Mr Heydon encouraged Mr Shorten to curb some of his "extraneous" responses and try to answer questions directly.

"I do think some concentration on your part, on giving a proper answer, as full an answer as the question demands but no more than that, is in your interests and it's something [counsel assisting the inquiry Jeremy Stoljar] is entitled to," he said.

Labor frontbencher Brendan O'Connor criticised the commissioner's comments.

"It was a remarkable interjection, intervention, by the royal commissioner today to suggest that Mr Shorten should reduce his answers down to 'yes', 'no', or 'I don't recall'," Mr O'Connor said.

"He made some prejudicial comments about the appearance of Mr Shorten which I think calls into question the motives of the establishment of this royal commission.

"I've said all along this is a witch hunt."

Shorten should 'just go': former ALP heavyweight

Government frontbencher Eric Abetz hit back at the Opposition's criticisms.

He said he would not comment on specific cases, including Mr Shorten's, but most people had been "quite horrified" by some of the evidence the commission had heard.

"From the evidence that has come thus far, and the resignations that have come thus far, I think most Australians would say 'well some of these things need to have sunlight shone on them'," Senator Abetz said.

Meanwhile, a former Labor national secretary, Bob Hogg, used Facebook to attack Mr Shorten after his appearance on Wednesday, when he admitted he failed to declare an election donation worth tens of thousands of dollars.

The hearing was told Mr Shorten accepted more than $40,000 from labour hire company Unibuilt to cover the costs of an election campaign staffer in 2007.

His union was negotiating a workplace deal with the company at the time, and Mr Shorten did not declare the donation to the electoral commission until several days ago.

"Dear Bill - is the concept of conflict of interest beyond your understanding," wrote Mr Hogg, who was ALP national secretary from 1988 to 1993.

"Do something for the ALP. It is simple. Just go."

Outside the hearing, Mr Shorten dismissed both Senator Abetz and Mr Hogg's comments.

"Mr Hogg's advice I put somewhere between [Prime Minister Tony] Abbott's and Senator Abetz's and probably even [Education Minister] Christopher Pyne's," he said.

Mr Heydon said Mr Shorten could be called to appear before the commission again, and other interested parties may be given the opportunity to cross-examine him.

The commission's next hearing is in Canberra on Monday and will focus on the Construction, Forestry, Mining and Energy Union (CFMEU).

It is due to deliver its findings by the end of the year.