Genomic testing confirmed a fully-vaccinated traveller who arrived from the Netherlands via Abu Dhabi on Friday contracted the new variant, the health department said in a statement on Wednesday.

The traveller opted to be transferred directly to hotel quarantine and has not been in the community while infectious.

They returned an initial negative PCR test on Saturday before developing symptoms on Monday, when they returned a positive test result.

The source of infection remains under investigation and all other passengers on the flight are being followed up to ensure they have been tested, in line with current requirements for overseas arrivals.

The department is also investigating likely Omicron cases detected in the cities of Casey and Brimbank.

The two cases have returned results with S gene dropout - a signature of the Omicron variant.

"Household contacts of these cases have also tested positive and whole genome sequencing is underway to confirm whether these represent the Omicron variant," the department said.

"None of these cases are linked to international travel and their source of acquisition is under investigation."

Several contacts of the two cases have been identified and told to quarantine for 14 days, while lower risk contacts have been instructed to get tested and isolate until they receive a negative result.

Further tracing is ongoing and is likely to produce more contacts.

The department said their advice may change if genomic sequencing shows the cases are not infected with Omicron.

The variant, which was first observed in South Africa, has already been detected in NSW, the ACT and the NT.

It comes as Victoria reported 1312 new COVID-19 infections and a further five deaths.

It brings the total number of active cases in the state to 11,331, down from 13,050 on Tuesday.

There are 303 people battling the virus in hospital, 97 of whom are in intensive care and 27 requiring ventilation. The seven-day hospitalisation average sits at 297.

Testers processed 79,490 results on Tuesday, while 3858 people were vaccinated in state-run hubs.

More than 91 per cent of Victorians over 12 are fully vaccinated.

Meanwhile, the Victorian government has announced it will spend $21 million to establish a mRNA research program as part of its push to use the technology to manufacture vaccines on an industrial scale for future pandemics.

Australian Associated Press