Schools are hoping thousands of absent children will return to class this month.

Principals say 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 have lost so many children that principals fear their staffing and funding will be slashed next year.

Te Tai Tokerau Principals Association president Pat Newman says he surveyed members recently and all who responded are 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."

Attendance has always been poor in Northland, but Covid-19 has made it worse.

"People didn't want their kids here in case they caught Covid, 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 says many of the children will eventually return and they will need a lot of help to catch up on what they have missed.

He says schools can only do so much, and the wider community needs to tackle truancy too by taking school attendance more seriously.

Whāngarei Intermediate School principal Hayley Read says her school is missing about 100 pupils.

She says if they did not return before July 1 when schools reported their roll numbers to the Education Ministry, her school and many others in Northland will 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."

Read says it will be challenging to replace teachers once the missing students returned.

Te Tai Tokerau principals have 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 says it has 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."

Teddy says last week's $88 million boost for attendance and truancy will 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 says absences and homeschooling havr been reasonably significant for schools in the Western Bay.

Billington says some families interpreted mask and vaccination requirements as evidence that the Covid-19 situation is serious so they kept their children home.

Western Bay of Plenty Principal's Association president Suzanne Billington. Photos: John Borren/SunLive.

Some have applied for homeschooling and it's not yet clear how many will persevere with that, she says.

"Smaller rural schools it really impacts on because a few students means a loss of staff," she says.

"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 says she expects a lot of the missing children will 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."

The Education Ministry says as at April 30, 10,769 children had exemptions for home-schooling, with 845 applications pending a decision.

The figure was about 40 per cent higher than the middle of last year.

Auckland Primary Principals Association president Wendy Kofoed says the city's schools have lost a lot of children too and they are unlikely to return.

"Twenty per cent 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."

Kofoed says schools are grateful the Education Ministry has protected their government-funded teacher numbers this year and that has helped many schools cope with the pandemic.

But she says operations grant funding has 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."

-RNZ/John Gerritsen.