The ROC said it will appeal the decision.
"The effect of the orders made are that the documents seized under the search warrants will remain in the custody of the Australian Federal Police pending an appeal that the ROC intends to make to the Full Federal Court,"a ROC statement said."The ROC will not make any further comment on the matter at this time."
The AWU said the court order had brought an end to the investigation which was leaked to media outlets ahead of the federal police raids and seizure of documents from its offices.
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Acting AWU national secretary Misha Zelinsky welcomed the court's decision which found the raids unlawful.
"The ROC has already spent an extraordinary amount of taxpayer dollars and the extensive resources of the federal police on this illegal pursuit,” he said.
Maurice Blackburn principal Josh Bornstein,who is acting for the AWU,said the raids on the union’s offices were unprecedented.