The duo pointed the finger at the Department of Health and Human Services when they appeared before the state's hotel quarantine inquiry on Wednesday.

"It was a health emergency, therefore the control agency was DHHS," Ms Neville, the police and emergency services minister, told the inquiry.

Neither minister knew who made the decision to use private security in the program, rather than Victoria Police or the Australian Defence Force.

The inquiry has previously heard then Police Chief Commissioner Graham Ashton preferred private security, while Emergency Management Commissioner Andrew Crisp maintained there was no need for ADF "boots on the ground".

Ms Neville had a scheduled meeting with Mr Ashton and Mr Crisp at 2pm on March 27, immediately after national cabinet announced the hotel quarantine program.

"It was clear to me and I think to both commissioners that a decision had already been taken about the front line of enforcement at the hotels," Ms Neville said.

She said the use of private security "didn't jump out" as an issue immediately, noting contractors were used at parliament, hospitals and police headquarters, as well as at major events.

"Reflecting on the question now, there are clearly things that went wrong," she wrote in her submission to the inquiry.

"I do not know whether that was because of the use of private security at all, or because of issues with the management and oversight of the private security arrangements, infection control management, or both."

Jobs Minister Martin Pakula said while his department was tasked with contracting hotels and security companies for the program, the DHHS held "overall responsibility".

The contracts placed the responsibility of training guards, including in the use of personal protective equipment, on the security companies.

Hotels were responsible for cleaning, unless a returned traveller tested positive to COVID-19.

"I don't take from it a suggestion that there were no obligations on anybody else in addition to that," Mr Pakula said.

He said in hindsight, it would have been preferable for the DHHS to be in charge of the contracts.

More than 30 staff and guards working at two quarantine hotels - the Rydges on Swanston and Stamford Plaza - caught COVID-19 from returned travellers and spread it into the community.

Some 99 per cent of second wave cases in Victoria can be linked to the two outbreaks.

The inquiry previously heard guards received little to no training in appropriate PPE use and failed to adhere to social distancing rules.

Public servants in Mr Pakula's department had concerns about the program as early as April, but he wasn't aware of them until the inquiry was called in July.

By then, the Department of Justice had taken over the running of the program.

DHHS secretary Kym Peake also appeared before the inquiry, after earlier denying her department had "sole accountability" for the program.

It was revealed Ms Peake and her deputy Melissa Skilbeck denied a request from Premier Daniel Andrews to house passengers from the Greg Mortimer cruise ship at a hotel near the airport.

Eighty of the passengers were COVID-positive.

"Premier has also requested that we use a hotel that is close to the airport, not in the CBD," Ms Peake wrote in an email on April 9.

Ms Skilbeck replied: "At this late stage of planning it would be risky to seek to convince another hotel to contract to take such guests."

The passengers were sent to the Rydges on Swanston.

Ms Peake also failed to brief Health Minister Jenny Mikakos on two reports that identified problems with the program.

Ms Mikakos will front the inquiry on Thursday, while Mr Andrews will give evidence on Friday afternoon.

Australian Associated Press