Victoria's Chief Health Officer Brett Sutton said he was confident Victoria has passed the peak of its second wave, but does not expect the full effects of Melbourne's stage four lockdown to become apparent for several days.

"Stage four will only show in the numbers over the next few days," he said.

"We've turned the corner ... and we should see a further driving down of transmission with stage four restrictions, so it is going in the right direction and I'm confident we've seen the peak, but it's got to come down quickly."

He said Victoria would likely see fewer deaths as a result of the virus over coming weeks, despite outbreaks across at least 125 aged care homes.

"If we can drive numbers down from here on in ... we should see a stabilisation of deaths in the next couple of weeks. We are concerned about the significant number of aged care cases, over 2000. They are most at risk of dying. We also have to drive those numbers down as well," he said.

One in five cases are 'mystery cases'

However one in five cases of COVID-19 in Melbourne are "mystery cases", where the source of a person's infection cannot be identified, Professor Sutton revealed.

The majority of mystery cases are among people aged 20 to 29, he said.

Health authorities have identified 51 new mystery cases in the past day, bringing the state's tally of infections from unknown community transmission to 3119.

"Certainly we've seen a significant increase in the so-called mystery cases, or cases of unknown acquisition," Professor Sutton said.

He said contact tracers could not determine the source of infection for 20 per cent of cases in Melbourne and 13 per cent of cases in regional Victoria.

"They don't have anyone in their household, who has been unwell, nobody in the workplace. The places they nominate don't have existing cases, clusters [or] outbreaks, so we can't determine absolutely where they got it from," he said.

"But we know there are other opportunities where people can pick it up. Sometimes they won't recall a close contact and sometimes they've had a more casual contact."

However, Professor Sutton said cases of unknown community transmission had plateaued in the last week. "That is related to a plateauing of overall cases," he said.

Professor Sutton said the role of asymptomatic cases in driving unknown community transmission was still not clear.

"Truly asymptomatic people probably don't commit much to transmission at all. What we're concerned about is people who have presymptomatic illness.

"In the two days before [someone] develops symptoms, they ... can be highly infectious ... so some of those mystery cases will absolutely have been exposed to someone who is presymptomatic."

Yet he believes 80 per cent of Victoria's cases are being identified.

"With 7000, 8000 active cases, it becomes harder to know the ones that aren't being identified, but I think it's the great majority."

Professor Adrian Esterman, chair of biostatistics at the University of South Australia, has said he is "100 per convinced" Victoria has passed the peak of its second wave.

"If you look at the trend over the past week, it seems to be unmistakable – it’s going down," he said.

The seven-day rolling average of new cases has dropped from a peak of 575 almost two weeks ago to 310 on Thursday.

The effective reproduction number – which measures the average number of people each infected person passes the virus on to – has also fallen to 0.74 according to a model by Professor Esterman. If the number remains below 1, case numbers will continue to fall.

But the Andrews government remains under fire over failures in the state's hotel quarantine program which has been identified as the source of the state's second surge in cases.

The Age and The Sydney Morning Herald revealed on Friday that patient zero in Victoria's calamitous second wave of COVID-19 was not a badly behaved security guard but a night duty manager at the Rydges hotel on Swanston Street, one of Melbourne's busiest quarantine hotels.