They had argued for a civil case involving the state to be put on hold until the criminal one against the health department progresses.
But Victoria's Court of Appeal shot down the challenge on Tuesday.
The criminal case is before the Victorian County Court, where the department is charged with 58 counts of breaching Occupational Health and Safety laws.
Businesses in a civil class action are arguing the state breached a duty to take reasonable care implementing infection control at quarantine hotels, resulting in the community spread of COVID-19 and a 112-day lockdown.
The two cases have been described as similar.
In an appeal hearing, the state's barrister David Neal SC said civil procedure requirements to provide a defence to the claims, including anything which might take the plaintiffs by surprise, would "send shivers down the spine of a criminal lawyer".
He suggested there would be prejudice to the state if required to share that defence with others before details of the criminal case are finalised.
"We do not have to tip our hand to a party who is hostile to our interest prior to hearing what the criminal case is," Dr Neal said.
But Michael Borsky KC, representing the class action businesses, said the state had not been ordered to file a defence - only to confidentially serve a proposed defence.
It was suggested the confidentiality order put in place by Justice John Dixon would protect the information from being used by anyone outside Mr Borsky's legal team.
In a unanimous judgment, three appeal justices found against the state.
"Given the limit of the judge's orders, and the steps taken by him in those orders to ensure the state is not compelled to assist the prosecution in the charges against it, it cannot be said that His Honour's decisions or orders are unreasonable or plainly unjust," they said.
Prosecutors in the criminal case are expected to present their written case in late June.
It had been suggested the state would seek to have the case lifted to the Supreme Court in the hope of a trial being heard before the end of the year.
