A new strain of Omicron that's spreading in NSW could see COVID-19 cases double within weeks.

Health Minister Brad Hazzard appeared at a budget estimates hearing on Thursday as the state recorded 16,288 new cases, an increase of more than 3000 on the previous day.

"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," he said.

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

Data from the University of NSW suggests Omicron's BA2 sub-variant is more transmissible.

Mr Hazzard is also concerned people have become complacent about getting a booster shot, with just 56.3 per cent of people having had three vaccine doses.

"While the community may have gone to sleep on the virus, the virus has not gone to sleep on the community," he said.

"The virus can still wreak havoc if we don't go out there and go and get our boosters fast."

Acting Chief Health Officer Marianne Gale said the technical term for the Omicron BA2 sub-variant is a "sublineage" and the dominant form of that in NSW had been BA1.

"What we are seeing ... is a trend to an increasing rise in the BA2 sublineage," she said.

"Experience has shown us overseas that BA2 can quite quickly overtake BA1 to become the dominant sublineage."

The sublineage was more transmissible but there was no evidence it was more or less severe, she said.

Meanwhile, there are concerns about health resources in the flood-ravaged communities in northern NSW.

One of the six evacuation centres in northern NSW could be converted into a COVID-19 isolation facility to deal with cases there.

Evacuated flood victims in northern NSW who have tested positive are being housed at Casino District Hospital, the hearing was told.

NSW Health's acting Deputy Secretary for Patient Experience and State Health Services Disaster Response Wayne Jones said the government is considering turning the evacuation centre at Goonellabah Sports and Aquatic Centre into a specific COVID-19 isolation centre for flood victims.

Mr Hazzard said the government was trying to ensure virus-positive people arriving at evacuation centres will be cared for in a safe location.

Dr Gale said cases have been reported at evacuation centres, but there have not been outbreaks.

NSW Health reported the deaths of two women and two men in the 24 hours to 4pm on Wednesday.