The NSW Department of Primary Industries estimates the deadly parasite could cost Australian beekeepers $70 million a year if it takes hold.
The destruction of hives and bee colonies began on Monday in identified eradication areas.
As of Friday, 99 infested properties had been identified in Newcastle, Port Stephens and the Central Coast region.
All hives and bees in the eradication zones will be destroyed, regardless of whether or not they have varroa mites.
No new hives can be established in the eradication zones for at least three years.
The department's chief plant officer Satendra Kumar says the destruction is necessary, and acknowledged beekeepers are facing a challenging period.
"They are at war for the rest of the country," Dr Kumar said on Wednesday.
He estimated the hives will be destroyed by the end of September.
Dr Kumar updated the emergency order on varroa mites this week as the destruction of bees and hives began.
The next phase will look at feral hives.
About 600 reports of feral hives have been made to the DPI so far, although Dr Kumar notes some could be repeat notifications.
Baits could be used to target those hives, after the managed hives are destroyed.
Some countries around the world did not even bother trying to contain varroa.
"They didn't even attempt because by the time they got it, it was pretty widespread," he said.
"It's very hard to manage this pest."
Dr Kumar said it was vital NSW eliminates the mite, which was first detected in biosecurity hives at the Port of Newcastle in June.
"If it was found everywhere, then obviously we would be out of the eradication and in a management frame, but at this stage we are confident the mite is quite limited," he said.
Reimbursement packages are in place for recreational and commercial beekeepers whose bees are destroyed.
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