Opposition Leader Bill Shorten has faced a slew of conflict of interest allegations over informal deals struck with employers which delivered millions of dollars to the Australian Workers Union while he was secretary, during a gruelling second day before the trade union royal commission.

And his political difficulties are unlikely to have finished, with another appearance expected before the commission in the coming months.

After leaving the commission hearing, Mr Shorten told the media he relished the opportunity to talk about his record of standing up for workers and that he would "put my record up against that of Mr Abbott's any day of the week."

"I seek to offer myself as the alternative prime minister of Australia. I am prepared to have my record of standing up for Australians put on display and before this next election we will be asking the same of Mr Abbott and his Liberals," he said.

Asked about former ALP national secretary Bob Hogg's call for Mr Shorten to resign as party leader, Mr Shorten said: "Mr Hogg's advice I put somewhere between Mr Abbott's, Senator [Eric] Abetz's and probably even Christopher Pyne's."

Chief among the deals examined on Thursday was $300,000 in payments by construction giant Thiess John Holland - revealed last month by Fairfax Media - after Mr Shorten struck a workplace deal that cut conditions, and saved the company as much as $100 million, on the $2.5 billion EastLink road project in Melbourne.

The royal commission also grilled Mr Shorten about millions of dollars paid by major employers including ACI, Huntsman Chemicals and Chiquita Mushrooms, to the AWU for what the union claimed to be paid education leave.

In a further blow to Mr Shorten, Commissioner Dyson Heydon warned that his credibility as a witness was at risk and chastised the Labor leader for using the inquiry as a political platform.

"What I am concerned about more is your credibility as a witness ... it is in your interest to curb these, to some extent, extraneous answers," he said.

The comments prompted a furious response from Labor workplace spokesman Brendan O'Connor, who said the "remarkable intervention" constituted "prejudicial comments about the appearance of Mr Shorten, which I think calls into question the motives of the establishment of this royal commission".

After leaving the royal commission, Mr Shorten said: "Mr Heydon has a job to do".

"I get that. This is Tony Abbott's royal commission, but I am more than satisfied with the opportunity to put forward the case for Labor and the case for standing up for workers," he said. 

In many cases the companies were in the process of, or about to commence, enterprise bargaining agreements setting future wages and conditions for employees and members of the AWU - prompting questions from counsel assisting the commission Jeremy Stoljar about a conflict of interest over side payments made by companies when his union was negotiating such agreements.

Mr Shorten categorically rejected those conflict of interest claims, but he faces further scrutiny in particular over a side deal with EastLink builder, the Thiess John Holland joint venture, after he struck a flexible workplace agreement that saved the company tens of millions of dollars.

The payments form Thiess started soon after work began on the $2.5 billion EastLink tollway in Melbourne's eastern suburbs in 2005.

That deal was hugely favourable to the builder, allowing it to effectively work around the clock by reducing conditions around rostering and weekend work, helping the project finish five months early.

Mr Shorten, for his part, defended the deal, which was lauded in a 2006 report by the free enterprise lobby, the Institute of Public Affairs, as the best deal possible and one which took account of the need for flexibility.

Internal AWU documents, and emails between the joint venture and the union, point to an informal agreement under which the company agreed to pay the union $100,000 plus GST over three years.

The union then created what Mr Stoljar described as "bogus" invoices for services, training and events, and issued to Thiess to justify the $300,000.

"I would never be party to issuing any bogus invoices. Full stop," Mr Shorten fired back.

He negotiated the workplace agreement but he said he did not recall a deal for $300,000 in side payments to the AWU.  "I don't particularly remember having discussions," said Mr Shorten.

"I  did not involve myself in formulation of the charging of services for training, for education or any other matter," sheeting it home to then AWU Victorian state secretary, Cesar Melhem.

Mr Shorten also faced detailed questioning over an employment deal between the AWU and the company Chiquita Mushrooms that lowered wages for hundreds of mushroom pickers in return for unusual payments to the union.

Questions were raised about $4000-a-month payments the union received over six months in return for what the union claimed was for health and safety training

Last year, Chiquita Mushrooms' former manager Stephen Little said he could only recall one training session that lasted "an hour and a half or two hours at most".

Mr Stoljar put it to Mr Shorten that Chiquita's payment was being made to avoid industrial disruption - not for education, which Mr Shorten disagreed with - while the Labor leader was also probed about a Chiquita enterprise bargaining agreement that was struck as the company struggled with WorkCover premiums that had risen to $6.2 million because of injuries to workers.

Mr Shorten said Chiquita started to use a labour hire company to reduce its WorkCover premium and defended the deal that saw Chiquita employees move to the labour hire company over time, though some jobs were lost.

"If you're saying we should never do an agreement where we ignore the realities of the employer's balance sheet and ignore the injuries going to workers well, it's just not how it works," he said.

A controversial deal Mr Shorten oversaw under which Melbourne builder Winslow constructors paid his union hundreds of thousands of dollars over a decade for its employees' union dues was also examined.

The deal, revealed by Fairfax Media last month, was criticised by current AWU state secretary Ben Davis, who told the royal commission last month that it had  "profoundly" weakened the union's industrial position in the workplace and that he had ceased the practice.

Asked about Winslow's payment to the union for its workers' membership fees, Mr Shorten said it was his preference that union members pay their own dues but that "if the choice came down between someone being in the union and if their employer wanted to pay it as opposed to no one being in the union or the person not being in the union then I have no problem with that".

Mr Stoljar then put it to Mr Shorten that it made it difficult for a union to "go hard for its members" when it was receiving money at the same time from the employer.

"I'm not sure that's borne out by the circumstances of the industrial arrangements," Mr Shorten said.

Outside the commission, Mr Shorten denied he had acted with any conflict of interest as a union boss and said he always ensured his members were signed up and that "we knew who they were".

Earlier, Mr Hogg had called for the Opposition Leader to stop "defending the indefensible" - referring to the fact the labour hire company Unibilt paid for Mr Shorten's 2007 campaign manager Lance Wilson, which was revealed at the commission on Wednesday - and said he should "just go".

Supporters of Mr Shorten quickly fired back, pointing out Mr Hogg's own court appearance for failing to disclose political donations in 1991.

And Labor strategist Bruce Hawker said it was inevitable that when the Abbott government set up a royal commission into trade unions it would identify some cases of questionable conduct.

"In the case of Shorten, I don't think it's more than questionable. I don't think there's any evidence of criminality," he said.

"What it reveals is sloppy record keeping of donations which is a common occurrence of businesses, including businesses that donate to the Liberal Party as well."

He did not back Mr Hogg's calls for Mr Shorten to resign as leader.

"I just don't think there's evidence there to support that proposition," he said.

"If you had a royal commission into the Liberal Party and donations from the business community you'd have a front page story every day of the week

"If you're really serious about getting these sorts of issues addressed you wouldn't just look at individual cases, you'd look at the whole lot across both political parties."

Federal Employment Minister Eric Abetz said that after two days of hearings, "I think the Australian people would say some of these things did need to have sunlight shone on them, and that is what's occurring".

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