The second coronavirus wave in Australia's worst-hit state, Victoria, has been attributed to Melbourne's bungled hotel quarantine. And there are now concerns of a repeat disaster.

An inquiry into Victoria's hotel quarantine programme has wrapped up its evidentiary phase after testimony from former state Health Minister Jenny Mikakos and Premier Daniel Andrews last week.

In submissions made on Monday, counsel assisting the inquiry Ben Ilhe said the inquiry could "comfortably find that the hotel quarantine programme in Victoria failed to achieve its primary objective".

Therefore, he said, hotels became "a feeding ground for the spread of Covid-19 in the community".

"The failure by the hotel quarantine program to contain this virus is today responsible for the deaths of 768 people and the infection of 18,490 [people]," he said.

The comments were a damning assessment of the handling of the programme — a programme the premier insists was being overseen by his former health minister.

He says changes have been made to ensure the safety of Victorians in hotel quarantine, but as the state drops below 300 active cases for the first time in months, there are fresh concerns.

It emerged this week that as many as nine hotel quarantine workers could have contracted coronavirus at work since late July, rather than in the community, as had been previously thought.

Of the nine who became infected, five of them were Spotless employees, one was a Department of Health and Human Services staff member and two worked for Alfred Health.

Victoria's Deputy Chief Health Officer, Allen Cheng, told reporters on Thursday that investigations were under way to determine exactly when and how the nine became infected.

"We know that it's not part of one big outbreak because they're in different times and different places but I understand that the investigation is ongoing," he said.

The ABC reports that Spotless workers at the Novotel Melbourne South Wharf hotel were stood down in the middle of a shift on Wednesday amid concerns about infection control.

Opposition leader Michael O'Brien shared concerns about a third wave being started in Victoria, saying it is "absolutely disgraceful" for DHHS to continue to use private contractors in a hotel quarantine setting.

"After 800 deaths, the least we deserve from this premier is honesty and competence and this story shows that we've got neither," O'Brien said.

"To think that he's still got private security guards in hotels, still not doing proper infection control, still putting the community at risk, this is a government that just won't listen and just won't learn."

But Chief Health Officer Brett Sutton is insisting he will wait for the results of genomic testing before assuming the workers were infected on the job.

"If genomic testing comes through that indicates otherwise we'd reassess on that basis, but that hasn't come through yet," he said.

"We've had 20,000 cases in Victoria, they've been in staff settings as cleaners and as security, but have picked it up in the community."

Andrews, who has overseen a rocky few weeks of driving case numbers down, says the hotel quarantine programme is going through a process of change.

"It's not necessarily settled and it'll continue to evolve," he told reporters.

The hotel quarantine inquiry is expected to hand down its findings in November.