Geoffrey Watson SC was repeatedly challenged on Friday on his methods and his conclusions by Ruth O'Gorman KC, representing former Queensland CFMEU official Michael Ravbar.
Mr Watson pushed back when Ms O'Gorman suggested he was assembling information to paint a picture of the CFMEU as a violent organisation.
Mr Watson passionately defended his report.
"I remember so vividly coming to Queensland to start this investigation, having read all the preparatory material submitted to me, and thinking 'this is a beat-up'," he told the inquiry.
"I just looked at this and thought, this is mainly about schoolyard bullying, and then I started interviewing people and I had grown men, tough men, breaking down in tears.
"I was not assembling a case against them, just the opposite. I was assembling evidence."
In an often fiery day of testimony, Ms O'Gorman cross-examined Mr Watson over an incident he said was an example of the union's misogyny.
Referring to posters that read "Flush Labor down the toilet", accompanied by an image of a tampon in the bowl, Ms O'Gorman asked whether Mr Watson agreed another reasonable view could be that the posters were "female-centric".
"No," Mr Watson said.
Ms O'Gorman then asked whether Mr Watson regularly checked in women's toilets to see the posters put on the doors.
"I wonder if I'll be arrested," replied Mr Watson.
"I did take permission this morning, in circumstances where we checked first, but I used the ladies' toilets in this very building.
"But there was nothing on the walls ... please don't put that in the paper," he said, indicating to the assembled journalists.
"I'll leave that alone," Ms O'Gorman said, smiling.
But Mr Watson did not back down from his original assessment.
"Women were attacked, women were stood over, women were abused, and putting that sign up with 'flush Labor down the toilet', I don't care what anybody says, that's obviously sexist," he said.
"It was repeated, it was relentless, they never gave up."
The exchange came towards the end of a day of cross-examination during which Mr Watson had earlier threatened never to return.
He later walked back his words, saying he would return if summoned.
Earlier, Mr Watson had sparred with Simon Wilson KC, for the M1 Trades Group.
Mr Watson had alleged M1 Traffic Control QLD Pty Ltd, owned by Michael Portia and Tony Paragalli, was in fact controlled behind the scenes by Melbourne associate Mick Gatto.
Both Mr Portia and Mr Paragalli vehemently denied the claims in an affidavit.
Exchanges between Mr Watson and Mr Wilson became so heated, Commissioner Stuart Wood KC advised them to cool off ahead of the morning tea adjournment.
"Both you and Mr Watson are very experienced silks, you know what the rules of engagement are," he said.
Mr Watson also told the inquiry the Victorian government never contacted him about the explosive contents of his report Rotting from the Top, which led to the downfall of former premier Jacinta Allan.
Ms Allan's Labor government had been publicly critical of Mr Watson following the release of his report, which detailed corruption surrounding its Big Build, a $100 billion construction project that began under former premier Dan Andrews.
Mr Watson estimated the alleged corrupt conduct by the CFMEU and Mr Gatto, a self-styled construction industry "mediator", had effectively fleeced Victorian taxpayers of $15 billion.
At his first press conference as premier, Ms Allan's successor Ben Carroll announced the Victorian government would hold a royal commission into the construction sector and the CFMEU.
