Victoria's Chief Health Officer says he first learnt about major problems with security contractors employed to guard Melbourne's quarantine hotels when he read it in newspapers.

A $3 million judicial inquiry is now investigating the links between Victoria's second coronavirus wave and the hotel quarantine program, which was designed to shield the state from the virus by placing returned travellers in 14-day isolation in hotels manned by private security companies.

Chief Health Officer Brett Sutton on Friday.Credit:Justin McManus

Professor Brett Sutton has previously revealed that genomic sequencing carried out by Melbourne's Doherty Institute shows a significant proportion – if not all – of Victoria's second-wave cases may be traced back to quarantine breaches at hotels.

Premier Daniel Andrews and his ministers have come under fire over security guards who became infected with the virus, and their refusal to reveal further details about the scheme due to the ongoing inquiry.

Former judge Jennifer Coate, who is running the judicial inquiry, insisted this week that there was no reason for the Premier not to reveal all the information he holds about the botched program now.

In light of Justice Coate's comments, Professor Brett Sutton was asked on Friday when he first became aware of serious problems in the program.

Security guards at the Stamford Plaza in the Melbourne CBD have been linked to a coronavirus outbreak.Credit:Getty Images

Professor Sutton and other senior public health officials were told about inadequate supply of masks and gloves, poor infection-control protocols and breaches of physical-distancing guidelines by hotel staff, security and health personnel.

Security guards and health workers at the Rydges on Swanston and the Stamford Plaza cited the same problems raised with Professor Sutton as the cause of coronavirus transmission at both hotels.

When asked whether Victoria could have eliminated the virus had the breaches in hotel quarantine not happened, Professor Sutton said it was "impossible to say". But he noted there was no genomic evidence to show that any of the state's current active cases could be traced back to the virus circulating in February, March or April.

"There’s no evidence of the original virus in the genomics, but not everyone has been tested," he said.

Professor Sutton also added that the Stamford Plaza outbreak was "more constrained" than the Rydges outbreak, but he did not know the current tally of cases linked directly to those clusters.

"[It was] when the genomics report came through when I was aware that a very significant proportion of our current cases were linked to hotel quarantine. It was information that was only available when that genomics report was through," he said.

Professor Sutton has previously said he played no role in the snap decision in May to draft in three private security firms to guard the hotels.

The inquiry into the hotel quarantine program has been delayed due to Melbourne’s stage four lockdown and will not deliver its findings under November 6, six weeks after its initial deadline. The first public hearings, which were due to start this week, will be held on August 17.

Professor Sutton has vowed to stay in his position until the end of the pandemic. His pledge followed inaccurate reports this week that he had resigned as Chief Health Officer due to tensions with the Premier.

He said he had "no idea" how the rumours, which were first reported by Sky News, emerged earlier this week. "It was a complete surprise to me," he said of the rumour.

"I will see us through this pandemic."

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