Schools have also been told to maintain good hygiene, ventilate classrooms and shared spaces, contact trace, and get those unwell tested.
Added anxiety is that schools and kura have the right to request information about the vaccination status of learners for their records, but unvaccinated students cannot be excluded.
Vaccination for the youngest eligible children began only on January 17, but none are yet eligible to be double-dotted. It is estimated almost 95,000 5 to 11-year-olds have now received a first dose - only one in five eligible (19.95 per cent). There are questions over how effective the paediatric dose is against Omicron.
There's also heightened apprehension among students. Many have spent two years moving in and out of lockdowns, particularly in Auckland where most students spent more than three months in isolation.
A report by 10 paediatricians report the harms from this disruption include poorer mental health, loss of learning and relationships, poverty, overcrowding and worrying high levels of family violence and abuse.
Largely unable to recruit from overseas has also left many schools struggling to compile a full staffing roster, even before the expected wave of sick leave when Omicron spreads.
There are reasons to take heart, however.
Starship developmental paediatrician Jin Russell points out schools are not high-risk for transmissions compared with restaurants, churches or workplaces.
Schools are also considered by some vulnerable children as a safe and trustworthy environment. They will benefit from being back in class.
And even a first dose of the vaccine provides excellent prevention against needing hospital time.
Respected modellers predict Omicron to peak in mid-February and tail away in March. Touch wood, schools can then get on with helping nurture Generation Covid.