All beehives within the identified eradication zone, including parts of Newcastle, the Central Coast and Port Stephens regions, will be destroyed, including those free of the varroa mite.
The destruction is necessary to fully eradicate the mites, NSW Department of Primary Industries chief plant protection officer Satendra Kumar says.
"It is critical that we look beyond just the known infected sites and eradicate any potential future hosts where incubation of the parasite may be happening," Dr Kumar said.
"Eradication activities will begin on the outer edges of the varroa mite eradication red zones and work towards the centre."
The eradication's next phase comes as two more infected premises were identified in the state on Friday.
It took the state's infected premises to 99.
Agriculture Minister Dugald Saunders also announced on Friday that beekeepers who had their hives, honey or equipment destroyed would be eligible for reimbursement.
Recreational beekeepers can claim $550 per hive, with commercial operators to be reimbursed at least the estimated market value of their hives and honey.
The newly identified premises are both close to existing infected premises.
"All confirmed cases either have clear links to existing cases or are geographically related," the DPI said on Saturday.
The mites were first detected in biosecurity surveillance hives at the Port of Newcastle in June.
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