Former deputy chief medical officer Dr Nick Coatsworth said the border policy was inconsistent due to the new variant being detected in other countries Australia has open travel with.

"It's proven that Omicron isn't just in southern African states, it's also in Europe, it also may well have been in the Australian community," Dr Coatsworth told Sky News.

"It may be elsewhere in the world that we have open borders to, then the consistency of the policy of shutting travel borders to certain African states starts getting called into question."

Australia banned flights from nine African nations in the wake of Omicron.

The new variant has led to a pause on the return of international students and visa holders, while all other international travellers have to undergo quarantine measures.

There have been 13 cases of Omicron detected in Australia, 11 of them in NSW, one in the Northern Territory and one in the ACT.

Globally, more than 400 Omicron cases have been identified in 30 countries.

While he understood the precautionary measures being taken, Dr Coatsworth said the new variant was likely to be milder than other strains of COVID-19.

"There's nothing that suggests that the vaccine is not working for the Omicron variant," he said.

"We do need to be concerned about the variants but we shouldn't become over-concerned when the early evidence is that this particular variant is more mild than the Delta."

Dr Coatsworth said it was unlikely there would be a new overly lethal version of the virus, and called for a more balanced approach in dealing with the new variant.

Meanwhile, health authorities have decided not to shorten the time frame in which people are advised to get a COVID-19 booster shot.

The Australian Technical Advisory Group on Immunisation determined people would still have to wait six months to get their third dose, due to earlier boosters not being proven to provide extra protection against Omicron.

Chief Medical Officer Paul Kelly said it was too early to determine whether Omicron would result in increased hospitalisations or deaths.

However, he said there was evidence it was the same as, or milder than, current variants.

Australia is likely to pass half a million booster doses on Saturday, with the current tally sitting at 495,000 third doses.

The NT recorded its first COVID-19 death on Friday, an unvaccinated woman from a remote Indigenous community.

There have been three remote communities in the Top End where the virus has been detected.

Victoria on Friday recorded 1188 new infections and 11 more deaths.

NSW reported 337 new cases, while there were four infections in the ACT and SA and one in Queensland.

Australian Associated Press