Worksafe has charged the Department with 58 breaches of the Occupational Health and Safety Act.
WorkSafe alleges that those working in hotel quarantine, including Health Department employees and security guards, were put at serious risk of illness or death through contracting Covid-19 from an infected returned traveler, another person working in the hotels or from a contaminated surface.
The maximum penalty for each of the charges is $1.64 million.
In a statement, Worksafe says its investigation took 15 months to complete and involved reviewing tens of thousands of documents and multiple witness interviews.
The matter will go to the Melbourne Magistrates' Court on 22 October.
Nearly 800 people died from Covid during Victoria's second wave, and more than 18,000 people caught the virus.