"We request that Victoria Police is present 24/7 at each hotel starting from this evening. We ask that DHHS urgently make that request as the control agency," the email read.

DHHS was asked to address issues on the supply and distribution of masks and gloves, and to clarify policies on whether detainees could leave their rooms or order UberEats takeaway food.

The email was also sent to Emergency Management Victoria, which was jointly responsible for the hotel scheme alongside DHHS.

The Age and The Sydney Morning Herald have chosen not to reveal the identities of those named in the email exchanges, or to quote from the emails in full, because those involved had not consented to providing the emails to the media.

Premier Daniel Andrews announced an inquiry into Victoria's quarantine scheme, to be led by former judge Jennifer Coate, after protocol breaches by guards at the Rydges on Swanston and Stamford Plaza hotels were identified as the source of coronavirus outbreaks in Melbourne's north and west.

The outbreaks marked the start of a second surge across the state. Victoria recorded 177 new cases of COVID-19 on Monday after more than a week of triple-digit daily increases. In May and June, there were dozens of days when fewer than 10 new cases were reported statewide.

The state’s Chief Health Officer said on Monday it was "conceivable" that all the active COVID-19 cases in Victoria stemmed from Melbourne’s problem quarantine hotel program.

After an incident in which a traveller left his room to smoke at 3am, the Department of Jobs, Precincts and Regions official sent a second email on March 30 demanding that DHHS request police support, suggesting private security companies were "not adequate" to guard the hotels.

The email recommended DHHS ban quarantined travellers from leaving their rooms for any reason, including exercise.

A top official from Emergency Management Victoria responded to the request by saying police were not required because guards could call triple zero if a situation warranted police involvement.

DHHS declined to answer questions about whether it requested the support of Victoria Police and whether its departmental officials escalated the concerns to Health Minister Jenny Mikakos. Victoria Police was contacted for comment but did not respond before deadline.

A spokeswoman for the Premier's office, also responding on behalf of departments, declined to answer questions about the early warnings, instead saying an inquiry had been established "at arm’s length from government", the same response it has given to questions on the failings of the hotel quarantine program since the inquiry’s establishment.

On July 2, the day the government announced a judicial inquiry, Police Minister Lisa Neville said police were not the default agency for the management of the pandemic response in Victoria, as they were in other states.

"Every state runs their emergency management system in a very different way. In NSW it’s run by the police ... that is not the case in Victoria. In health emergencies, it’s health."

On the same day, the Premier labelled the quarantine breaches "unacceptable". "It’s why there have been changes into the way hotel quarantine operates," Mr Andrews said.

The Age and The Sydney Morning Herald reported earlier this month that at least five agencies were involved in the decision to deploy private security guards, instead of soldiers or police, at quarantine hotels: Health; Jobs; Premier and Cabinet; Emergency Management Victoria; and Victoria Police.

Emails sent on March 29 and an internal Emergency Management Victoria operational document dated March 28 detail the roles and responsibilities of each agency in the hotel quarantine system, with DHHS and Emergency Management Victoria leading the program.

DHHS and Jobs Department worked together – along with the Department of Transport, the Australian Federal Police and Border Force – on the logistics and planning of the hotel scheme, including transporting travellers from the airport.

Wilson, MSS and Unified were the three major security companies contracted to provide security at the hotels.

A spokeswoman for Wilson Security – which says it did not supply guards at either Rydges or Stamford Plaza and says none of its workers were infected – said it collaborated with police for hotel site walk-throughs, and it defended its capacity to equip guards to work at quarantine hotels.

The company regularly "reinforced use-of-force provisions and legal authority for quarantine restrictions", the spokeswoman said.

"We deployed specialist services and expert personnel from our corporate risk department to oversee the deployment of all staff into hotels.

Drive host Rafael Epstein asked: "So it’s still [the case that] most, if not all, comes from the one problem in one hotel?"

"Yeah, that's conceivable absolutely," replied Professor Sutton.

The Chief Health Officer said he used "pretty colourful language" when the genomic link was first made between hotel quarantine and outbreaks around the city.

"No one wants to have that be the case. I felt that everyone who was managing that quarantine program, because they were actually doing a fantastic job managing all of the logistic complexities of it. But it speaks to, you know, the dangers of any positive case out there and the ability for it to spread very extensively as has occurred."