But while case numbers are expected to increase, authorities don't anticipate a dramatic rise in hospitalisations.

The acting ACT chief health officer, Dr Vanessa Johnston, said Canberrans should still consider wearing masks indoors when they were unable to socially distance, but stricter public health measures were not yet needed.

Planning is also under way to manage a winter wave of COVID-19 infections, including surveillance work to identify when new variants come into the ACT.

Dr Johnston said health authorities had thought the daily case rate of COVID-19 in the ACT would continue to decline before increased transmission in the winter months led to a new peak.

However, the emergence of the BA.2 sub-lineage meant case numbers would start to rise slowly sooner than expected, she said.

The BA.2 sub-lineage is more transmissible than BA.1 but there was no evidence it led to more severe disease, Dr Johnston said.

She said modelling from ACT Health indicated the increased caseload would not result in more hospitalisations.

"The modelling suggests that by the end of this week our case rate may increase to about 800 per day," Dr Johnston said.

"So we expect cases to increase slowly over the coming weeks but encouragingly our modelling is showing that our daily [hospital] occupancy is predicted to be around 36 so that's similar to what we're seeing now."

While BA.2 is more transmissible, Dr Johnston said those who had been infected with the BA.1 had protection against the sub-lineage. She said she did not expect there would be a surge like the Omicron summer peak.

"No one is anticipating the exponential growth that we saw with Omicron BA.1 because we were all completely naive to it," she said.

"With the level of natural and vaccine-derived immunity, we're not going to see that exponential growth from BA.2 but should we have any new variant coming into the country then I think we need to reassess."

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NSW Health Minister Brad Hazzard on Thursday told a budget estimates inquiry health authorities in that state expected COVID-19 case numbers would double in the coming weeks.

"Preliminary information indicates that ... in only another month to six weeks we could be looking at cases more than double than we are currently getting," Mr Hazzard said.

"It is concerning us greatly, that we are seeing an increase in daily cases."

A spokeswoman for ACT Health told The Canberra Times in a statement on Thursday evening that a third of sequenced COVID-19 samples in Canberra over the last week had the BA.2 sub-lineage.

"As this is not a random sample of cases, we are unable to say if this is representative of what is occurring in the community," the spokeswoman said.

Less than 10 per cent of cases identified in the ACT are presently being sequenced to determine the virus strain. Hospitalised cases, high-risk setting outbreaks and returned overseas travellers are prioritised for sequencing.

The spokeswoman said the ACT had seen a slow increase in daily cases, which had come after community movement increased and further public health measures were wound back.

"This is likely due to a combination of factors including an increase in the case rate in the 5-11 year age cohort possibly leading to an in increase in testing in the 25-64 year age group from household and close contacts," the spokeswoman said.

The ACT reported 821 new cases of COVID-19 on Thursday. There were 37 people in hospital; two people were in intensive care, where one person was ventilated.

The World Health Organisation last month said the proportion of sequenced COVID-19 cases designated as BA.2 was growing relative to BA.1 while the global circulation of all variants was reportedly declining.

"Initial data suggest that BA.2 appears inherently more transmissible than BA.1, which currently remains the most common Omicron sub-lineage reported," the World Health Organisation said in a statement on February 22.

"This difference in transmissibility appears to be much smaller than, for example, the difference between BA.1 and Delta."

Infection with BA.1 provides strong protection against reinfection with BA.2, however cases of reinfection have been documented, the World Health Organisation has said.

In South Africa, the United Kingdom and Denmark, where immunity from vaccination or natural infection is high "there was no reported difference in severity between BA.2 and BA.1".

More to come.