The ministry's attendance service dealt with nearly 28,754 cases last year, 40 percent or 8600 more than in 2021.
Most of the cases - 16,400 - involved children who had been absent from school so long their enrolment had lapsed.
Principals told RNZ they hoped changes to the attendance service would bring the numbers down this year.
The ministry had nearly doubled the number of organisations contracted to get truants back to school from 45 last year to an expected 79 this year.
It said six organisations had left the attendance service, and 40 new ones were joining, many of them groups of schools.
The change followed longstanding criticism of the service in some areas and worsening attendance figures.
In Northland, where school attendance rates were the lowest in the country, the ministry signed up five new attendance service providers.
Te Manihi Tumuaki (Northland Secondary School Principals Association) chair Alec Solomon said the change was good because the previous system was not working.
"It's a really complex taki to deal with and try and understand what are the symptoms and what are the causes. We're pretty happy that we've got a new lens across it and we've got new support and we need it," he said.
"It's a real benefit that we're looking for local solutions to local problems and we're hopeful."
Maintaining good attendance last year was difficult, Solomon said.
Schools had told students to stay home because of Covid but that made it difficult when the time came to encourage them that it was safe to come to class, he said.
"That was somewhat problematic," he said.
Berkley Normal Middle School principal Nathan Leith was another who said the pandemic was part of the problem behind last year's poor attendance.
"We were telling kids 'if you are sick stay home, we don't want to have you at school, you need to stay home' and so as we slowly got through that, towards the end of last year we were then saying to families 'no, no, we need you at school'," Leith said.
"So I'm a little bit dubious about the doom and gloom around attendance. Sure, there are some issues there that we need to address, but I just wonder how much of it is off the back of Covid."
Leith said Berkley and nine other schools in a Kahui Ako, or formal cluster of schools, on the eastern side of Hamilton had combined to form one of the new attendance service providers.
The schools should be able to do a better job than the previous organisation because they worked with families every day, not just when attendance became a problem, he said.
"We, as a cluster of schools, meet weekly and we do talk about attendance issues and families who may need some extra support to get their children to school. When I mean extra support, things like lunches or food or sometimes uniforms, shoes, anything like that that might just be the thing that's stopping kids coming to school."
The Education Ministry said it had contracted more providers, including schools and iwi, because trials in Auckland and Kawerau showed schools wanted organisations that were local.
"This allowed for faster responses to referrals, a more direct line of sight between schools and the local attendance service provider, strong relationships with school leaders, family and whānau enabling more collaborative processes. Local providers are able to recruit attendance advisers from local communities who have a deeper better understanding of their own community and local approaches to address barriers to attendance and enrolment," it said.
Secondary Principals Association president Vaughan Couillault said in some areas such as his own, schools wanted closer control of their local attendance service and it seemed to be working.
"It's still quite early days in terms of that model being deployed in our region. I think it's providing a lot better response. It's a lot more responsive, a lot more innovative and a lot more flexible in terms of being about to meet the needs of our community," he said.
The attendance service dealt with 28,754 cases involving 23,522 children last year.
Sixty percent of the cases involved Māori students and 82 percent of the students were first-time referrals to the service.
The service helped 46 percent of the 12,639 "unjustified absence" cases it closed last year return to school, 14 percent had returned to school by the time the service caught up with them, and a further 20 percent were reclassified as non-enrolled.
It closed 14,115 cases of non-enrolment last year, 2287 fewer than it opened.
Of those it closed, 45 percent had already enrolled in a school, 24 percent were helped to enrol, and 17 percent turned 16 and were no longer required to attend school.