The union said it was forced to use $1 million of members' money to answer questions from the Commission; and now wants the money returned.
“The Transport Workers’ Union should never have been called before the Royal Commission. This final report refers to a matter which the TWU already had investigated and turned over to the appropriate authorities. No new information was found in the Royal Commission’s inquiry into the matter,” said Tony Sheldon TWU National Secretary.
Contentious laws cracking down on union misconduct will be reintroduced next year following a damning royal commission report.
Commissioner Dyson Heydon released his final report on Wednesday, with 79 recommendations and 93 referrals to authorities for further investigation.
He has referred the Australian Workers' Union and the former head of the union's Victorian branch, Victorian Labor MP Cesar Melhem, to prosecutors for possible corruption and false accounting charges.
A slew of other union officials, including former Health Services Union secretary Kathy Jackson, along with companies, executives and the NSW branch of the construction union have also been referred for investigation, with Mr Heydon finding union misconduct was widespread and "deep-seated".
The CFMEU has slammed the Trade Unions Royal Commission for making recommendations on safety without consultation.
Recommendations from the commission include changes to right of entry laws which permit union officials entering worksites in the event of safety breaches, after finding CFMEU officials sometimes ignored entry rules or abused Fair Work inspectors.
The report also identified six CFMEU officials to be referred to prosecutors.
National Construction Secretary Dave Noonan says neither he nor any rank and file members or developers were called to give evidence about working with the union to improve safety.
Mr Noonan has labelled the Commission as a witchhunt with a pre-determined outcome.
"This Royal Commission was set up to smear Julia Gillard, to smear Bill Shorten and to smear the Trade Union movement and all the pages if you read them - and I have read a lot of it - that's all it does," he said. "It's not about improving workers' rights."
Government gears up for election fight on unions
The Turnbull government will reintroduce laws rejected by the Senate to crack down on union misconduct following a damning report.
He believes what has been uncovered is just the "small tip of an enormous iceberg".
Prime Minister Malcolm Turnbull says the report is a "watershed" moment for Labor and its leader, Bill Shorten, to reform a union movement that has become concerned with self-interest rather than its members.
The government will reintroduce laws previously rejected by the Senate to re-establish the Australian Building and Construction Commission in the first week of 2016 and wants it passed before the end of March.
It will also reintroduce a stronger version of laws rejected by the Senate to set up a registered organisations commission, as recommended by Mr Heydon.
"We are willing to fight an election on this," Mr Turnbull said.
"We need the support of the parliament but if the parliament does not provide that support then obviously we will appeal, as we should in a democracy, to the people."
Employment Minister Michaelia Cash said crossbenchers who previously rejected the laws had indicated they were awaiting the commission's final report and she was confident the overwhelming evidence would get them on board.
Labor and the unions have dismissed the report as a political witch-hunt and insist any misconduct is isolated.