Construction workers who were charged after they walked off the job to attend a rally at the site of the Perth Children's Hospital contravened the Fair Work Act by their actions, the Federal Court has ruled.

Construction Forestry Mining and Energy Union officials addressed the rally on July 18, 2013 about wages, penalty rates and safety in relation to the project’s head contractor John Holland.

While the director of the Fair Work Building Industry Inspectorate initially targeted 101 workers, proceedings against 35 were discontinued.

Justice Michael Barker determined on Wednesday that allegations against 53 of the respondents had been proved, but had not been proved for 13 of the workers.

The CFMEU labelled the case “a complete waste of taxpayers’ money and an abuse of the justice system”, saying the workers should never have been prosecuted.

“If it were not for the support of their union, the 48 workers charged and not convicted would have had to engage lawyers, at great cost,” the union said.

“The few that have been convicted did nothing more than attend a meeting at the infamous state government children’s hospital project to be be informed of the workplace issues that the union identified more than three years ago.”

The project has been plagued by problems including delays and asbestos sheeting within roofing panels, sparking fears among workers who were exposed to the material.

Hundreds of them signed an “asbestos register” to monitor their health and possibly lead to compensation in the wake of the discovery.

Justice Barker ordered the matter be re-listed to hear from the parties what penalties, if any, should be imposed.