After a 15-month investigation, WorkSafe on Wednesday charged the Department of Health, formerly the Department of Health and Human Services, with 58 breaches of the Occupational Health Safety Act.

A filing hearing in Melbourne Magistrates Court is set for October 22.

Seventeen of the charges relate to failing to provide and maintain, as far as reasonably practicable, a working environment that was safe and without risks to health for its employees.

Another 41 charges are allegations of failing to ensure, so far as was reasonably practicable, that persons other than employees were not exposed to risks to their health and safety arising from conduct of its undertaking.

Between March and July 2020, the department was responsible for Operation Soteria, Victoria's first hotel quarantine program.

A judicial inquiry into the program found 99 per cent of the state's second wave could be traced back to security guards who became infected at the Rydges on Swanston and Stamford Plaza hotels in May and June.

The second wave resulted in more than 18,000 new infections, 800 deaths and a lockdown that lasted 112 days.

WorkSafe alleges the department breached occupational health and safety laws by failing to appoint people with infection prevention and control expertise at the hotels it was using.

It also alleges the department failed to provide security guards with face-to-face, expert infection prevention control training and written instructions on how to use personal protective equipment.

In all charges, WorkSafe alleges that Department of Health employees, Victorian government staff on secondment and security guards were put at risk of serious illness or death through contracting COVID-19 from an infected traveller, colleague or from a contaminated surface.

The maximum penalty for a body corporate for each of the charges is $1.64 million, or $95.12 million in total.

WorkSafe said the investigation reviewed tens of thousands of documents and multiple witness interviews.

It also reviewed material from last year's judicial inquiry into the scheme, which laid bare the disharmony within the ranks of the Department of Health and Human Services, leading to the resignation of the department's secretary Kym Peake and Health Minister Jenny Mikakos.

The inquiry found the department failed to accept its role as the primary department responsible, while senior members of the public health team, including Chief Health Officer Brett Sutton, were excluded from its planning.

The responsibility of training guards, including in the use of PPE, was placed on security companies, while the department only cleaned hotel rooms if a returned traveller tested positive.

A complete overhaul of hotel quarantine was announced in December, with a dedicated agency, COVID-19 Quarantine Victoria, established to run the program.

It was again revamped in April, after hotel quarantine workers contracted the UK COVID-19 strain from returned travellers in February, triggering a statewide five-day lockdown.

Opposition health spokeswoman Georgie Crozier described the hotel quarantine program as "the biggest failure in government administration in this state's history" and called for further resignations.

"Any minister who is still sitting around the cabinet table who was making the decisions in 2020 should resign and the premier needs to be held accountable and he needs to answer questions on this issue too," she told reporters.

Both Department of Health and Victorian government spokespeople declined to comment, citing the matter was now before the courts.

Australian Associated Press