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The border ban was to have been lifted to those groups of travellers on Wednesday, but Chief Medical Officer Paul Kelly has advised that be paused until December 15.
"The temporary pause will ensure Australia can gather the information we need to better understand the Omicron variant, including the efficacy of the vaccine, the range of illness, including if it may generate more mild symptoms, and the level of transmission," a statement from Prime Minister Scott Morrison's office said late on Monday.
"The reopening to travellers from Japan and the Republic of Korea will also be paused until 15 December."
Two fully vaccinated people who flew from southern Africa to Sydney were on Sunday confirmed to have the Omicron strain. They did not have any symptoms.
On Monday another two Sydney cases were confirmed - arrivals on a Singapore Airlines flight from southern Africa on Sunday.
Every other person who was on that flight is now a close contact who needs to get tested and isolate for 14 days immediately.
Separately, a man at the Northern Territory's Howard Springs quarantine facility was diagnosed with the strain.
The move follows the government's decision to ban the arrival of non-citizens from eight southern African nations.
Victoria, NSW and the ACT already have a blanket 72-hour quarantine requirement for all international travellers.
Health Minister Greg Hunt stressed Australia was well prepared for Omicron and contracts with vaccine manufacturers covered changes for new variants.
"There are some heartening signs about what may turn out to be mild symptoms," he told reporters in Canberra on Monday.
While the new strain appeared to be more transmissible, Professor Kelly stressed there was no definite evidence vaccines were less effective against it.
"The information from South Africa is that it has replaced Delta as the major, possibly the only, virus circulating in that country quite quickly. So it is transmitting at least as well as Delta. That seems clear," he said.
"Some reports out of South Africa are that it's mostly mild. Other information we have is that hospitalisation rates are increasing."
Federal, state and territory leaders are meeting as part of national cabinet on Tuesday afternoon to coordinate Australia's response to Omicron.
Mr Morrison defended attacks from Labor about the lack of purpose-built quarantine facilities, apart from Howard Springs.
Mr Morrison pointed to a facility in Victoria under construction as well as quarantine hubs planned in Western Australia and Queensland.
Meanwhile, the South African doctor who alerted authorities to Omicron warned the rest of the world wasn't safe until Africa was vaccinated.
"As long as we don't help and assist Africa no one will sleep well at night, not even Australia, North America and not Europe," Angelique Coetzee told ABC radio.
Nearly 87 per cent of Australians aged 16 and older are fully vaccinated.
Western Australia has the country's lowest full vaccination rate of 75.51 per cent, and it's unclear what Omicron means for the state's already tentative and conditional reopening plans.
"I don't know what's going to happen with Omicron. Omicron didn't exist until three days ago," Premier Mark McGowan told the ABC.
Victoria on Monday reported 1007 new COVID-19 cases and three additional deaths.
There were 150 new infections in NSW, seven in the ACT and two in the NT.