Mask-wearing in the classroom was a "big concern" for schools as principals prepare to open in the red traffic light setting.
Some school leaders said wearing masks indoors during summer would be "challenging" while others worried about whose responsibility it will be to supply them.
Prime Minister Jacinda Ardern announced the move on Sunday morning and expected the country to stay at red for "some weeks".
At this traffic light setting students Years 4 and up must wear face coverings indoors and when in close contact with others.
This included classrooms, assemblies and when accessing public venues.
Students aged 12 and over also must wear face coverings on public transport and school transport.
In a bulletin issued to school leaders on Sunday, the Ministry of Education said schools and kura would remain open at red.
Further guidance on the impacts of Omicron would be provided following Cabinet's meeting today
Principals were advised to prepare for delivering on-site and distance learning once school returned.
"I appreciate that some in your communities will have concerns about attending on site, as we have seen previously when settings are at their highest."
It was a slightly different start to the school year for Rotorua Intermediate principal Garry de Thierry, who normally was "full of enthusiasm".
"But I am sitting in my office trying to figure out who is responsible for supplying face masks and how we are going to manage the school."
He said mask-wearing was a "big concern" and the school would need to spend "thousands" on face masks if they were expected to provide them.
"I would love to have some guidelines from the Ministry," he said.
"We are just trying to get as much information as we can to put out to parents."
Despite the concerns, he said it was important that the start of the year was "settled" for the community.
"I am sure all principals are going through the same process of trying to be proactive to make sure it is a settled start to the year," he said.
"If it is a bit shaky that could impact on students and whānau throughout the year."
Ongoing news about Covid was putting "pressure" on students and they would need time to talk about this before learning got underway, he said.
"Every time they flick on the radio or watch something on TV there are a whole lot of alerts popping up about how bad this is going to be.
"When they get to school students will need time to talk and unpack before they get their head in the right space to think about engaging in learning."
John Paul College principal Patrick Walsh said the shift to red was not "welcome news" at the start of the school year.
"It was, however, inevitable and we have planned for it."
He expected it to be an "anxious time" for students and staff but said it was important to "normalise the return to school".
He said the school community had built up a "high degree of resilience", with the vast majority of students vaccinated and familiar with "distance learning".
"My key message to parents is to be positive and calm with your children. Don't let Covid disrupt your child's education."
He said it would be "challenging" wearing masks indoors during summer but expected students to be "very accepting" of the need for it.
John Paul College head boy Travis Dunningham believed the shift in settings would be "welcome news" to students as it ruled out further lockdowns.
"It is quite relieving that, at least in the short term, we won't have to worry about imminent lockdowns."
He said previous lockdowns had impacted the learning of some students who were "quite stressed" trying to keep up with schoolwork at home.
"I am used to learning in person or at home on Zoom. I feel like school will be pretty normal - the only difference will be mask-wearing."
He felt "absolutely fine" about having to wear masks on-site and believed his peers would share this sentiment.
"I don't mind wearing a mask, I do what I have to do. I think most people will be fine with it. But I do worry that younger students - even in our primary schools - will struggle."
The 17-year-old was also pleased some school events could still go ahead at the red setting - including their leadership camp in Tongariro.
Rotorua Principals Association president Gary Veysi said there were "big concerns" among some of the city's school leaders about the supply of masks at the red traffic light setting.
Whose responsibility it was to provide masks for school students was a "grey area" at the moment, he said.
"We have a surplus of masks at the moment. But they will be used up in days if we start giving them out to every child."
Classroom bubbles at Mamaku School - where Veysi is principal - would remain, with teachers and support staff staying in the same class.
"But that is limiting because that support staff member can't be going to other classes to help other kids."
He had also spoken to other principals about difficulties carrying out team building activities while following Covid protocols.
"The first part of the year is all about team building activities that you do together, they are close contact. You don't build your team being two metres apart with masks on."
But he felt school staff would "work through" the challenges and keep the school environment positive for everyone. Outside learning would play a large part in this, he said.
"For me, it won't be doom and gloom. This is something we have to work through. We still have a lot of things we can do."