Schools are hoping thousands of absent children will return to class this month.
Principals said one in five students were absent last term, many due to fear of COVID-19, fear of vaccinations and a rise in home-schooling.
In Te Tai Tokerau, schools had lost so many children that principals feared their staffing and funding would be slashed next year.
Te Tai Tokerau Principals Association president Pat Newman said he surveyed members recently and all who responded were missing significant numbers of children.
"For instance at my own school we are still missing about 80 children out of 300-and-something that should be here at school. Many of them we don't even know where they are, they're not in school, they're not in any school and that is a pattern that is in every school in Te Tai Tokerau and also I think wider than that," he said.
Attendance had always been poor in Northland, but COVID-19 had made it worse.
"People didn't want their kids here in case they caught COVID-19, others didn't want them at school in case we ran around with needles and injected them with the vaccination. We have many parents with every conspiracy theory you could possibly have in Te Tai Tokerau. So it's a whole combination."
Newman said many of the children would eventually return and they would need a lot of help to catch up on what they had missed.
He said schools could only do so much, and the wider community needed to tackle truancy too by taking school attendance more seriously.
Whāngarei Intermediate School principal Hayley Read said her school was missing about 100 pupils.
She said if they did not return before 1 July when schools reported their roll numbers to the Education Ministry, her school and many others in Northland would lose teachers and funding.
"That is a huge problem for us in Tai Tokerau because that means we're letting go very experienced teachers who have formed very strong relationships with our students," she said.
Read said it would be challenging to replace teachers once the missing students returned.
Te Tai Tokerau principals had asked the Education Ministry not to cut their staffing and funding next year if their enrolments did not recover.
The Education Ministry's hautū (leader) operations and integration Sean Teddy said it had met with Northland schools to talk about 2023 staffing.
"We have let them know that we will work with them on next steps, once July roll returns are received. We want to give as much certainty as we can about the situation for 2023 as quickly as we can," he said.
Teddy said last week's $88 million boost for attendance and truancy would help make the education system a place where learners wanted to be and where they could get the support they needed.
Western Bay of Plenty Principals Association president Suzanne Billington said absences and homeschooling had been reasonably significant for schools in her region too.
Billington said some families interpreted mask and vaccination requirements as evidence that the COVID-19 situation was serious so they kept their children home.
Some had applied for homeschooling and it was not yet clear how many would persevere with that, she said.
"Smaller rural schools it really impacts on because a few students means a loss of staff," she said.
"We hold on to staff until the end of the year but if those numbers don't return then it's possible that next year's staffing could be affected."
Billington she said she expected a lot of the missing children would return.
"We will probably see quite a number return over time because it is around anxiety about how safe schools are in this environment. I don't know whether that will happen straight away and so therefore it will have quite an impact on schools being able to plan and staff appropriately," she said.
The Education Ministry said as at 30 April, 10,769 children had exemptions for home-schooling, with 845 applications pending a decision.
The figure was about 40 percent higher than the middle of last year.
Auckland Primary Principals Association president Wendy Kofoed said the city's schools had lost a lot of children too, but they were unlikely to return.
"Twenty percent of students are down I think across the country and that's reflected in Auckland, particularly as Auckland has traditionally had thousands of workers and their families coming in from overseas, so that group has disappeared over the last two years and also we've had quite a lot of transience from Auckland out to communities, returning to home base to get more support," she said.
Kofoed said schools were grateful the Education Ministry had protected their government-funded teacher numbers this year and that had helped many schools cope with the pandemic.
But she said operations grant funding had not been protected.
"Our operation grants are going to be taking a hit this year and we're all sort of scrambling trying to make sure we've got enough staffing and that we're not reducing capacity in areas that our learners need, like support staff," she said.
RNZ
