The competition watchdog referred the Construction, Forestry, Maritime, Mining and Energy Union and its ACT boss, Jason O'Mara, for prosecution in 2018.

Both were charged as a result with two counts of attempting to induce businesses to engage in cartel conduct.

Mr O'Mara and the union pleaded not guilty, denying allegations they had pressed steelfixing and scaffolding businesses to collude on a fixed minimum price for their jobs in order to afford pay rises for workers in 2012 and 2013.

The charges followed an investigation by a taskforce established in response to the Royal Commission into Trade Union Governance and Corruption.

Prosecutors alleged, during a committal hearing earlier this year, that the union had threatened to "run out of town" anyone who did not go along with its alleged plot.

But the long-running case hit a major hurdle as the union and Mr O'Mara fought to have the charges thrown out without the need for a trial.

Their committal hearing was repeatedly disrupted by the disclosures of documents.

Revelations made in discussions outside court then called the future of the entire case into question.

Prosecutors eventually withdrew half the charges in February before doing the same with the remaining allegations in the ACT Magistrates Court on Tuesday morning.

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In a subsequent statement, the union's national construction secretary, Dave Noonan, said the allegations were "unsupported by the facts" and the charges should never have been laid.

Mr Noonan accused the ACCC of attempting to "weaponise the Competition and Consumer Act to attack the right of trade unions to collectively bargain".

"The federal government sank significant funds into this case, continuing its endless war against the rights of working Australians and the trade unions that represent them," he said.

Mr Noonan also claimed the competition watchdog had "engaged in the blatant victimisation of Jason O'Mara".

"An honest, hardworking trade unionist has endured three years of trial by media and attacks on his character," he said.

"[ACCC chairman] Rod Sims should apologise to Jason O'Mara and resign."

Mr Sims defended the prosecution in a statement issued by the ACCC, saying the Commonwealth Director of Public Prosecutions had made the decisions to commence and discontinue the case in line with the relevant policies.

"In this case, the decision to withdraw was made in the context of the extended period of time which has elapsed since the alleged conduct occurred, and the challenges that posed for witnesses' memories of relevant events," he said.

"While there can be challenges involved in bringing criminal cartel prosecutions, we will continue to place a high priority on deterring, detecting and dismantling cartels that can harm Australian consumers and businesses, and will continue to refer serious cartel conduct to the CDPP."

The ACCC declined to comment further.

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