The data from the ministry’s attendance survey, released under the Official Information Act, showed 66,029 half-days were missed by pupils due to unjustifiable absence last year. Year 1 to 6 pupils accounted for 28,012 of the half-days.
However, the figures show Otago and Southland had lower levels of unjustifiable absenteeism than the rest of the country.
The data from the ministry also showed the Otago-Southland attendance service provider investigated 375 cases of unjustified absence and 211 cases of children not being enrolled.
Ministry of Education deputy secretary sector enablement and support Katrina Casey said it was difficult to extrapolate from the data whether truancy was declining or increasing in Otago.
What was known was the importance of attending school, she said.
"Attending school is not just the law of the land up until the age of 16, it’s also the key to setting our young people up for life.
"Getting a qualification is one of the basic building blocks for success and regular attendance at school makes all the difference.
"For example, a year 11 student who only turns up at school half of the time has just a one-in-five chance of getting NCEA level 1. A student who attends every day has about a 90% chance of achieving that qualification."
Otago Youth Wellness Trust manager Barbara Payton said the trust was seeing more cases of family problems impacting on children attending school.
A younger cohort of pupils also appeared to be suffering from anxiety and mental illness, an issue not experienced in the past.
"One of the things we have noticed is some of the things we were seeing in years 7, 8 or 9 we are now seeing around years 5 and 6," she said.
"There’s definitely more anxiety in the younger age group."
The level of stress within family homes had increased, and the trust was witnessing that when working with young people and families. She agreed the level of unjustifiable absenteeism was troubling in the younger age groups.
"This is the kind of thing every community should be asking itself ‘why is this happening’," she said.
Otago Primary Principals’ Association president Debbie Smith also pointed to the comparatively low levels in the region compared to the rest of the country.
The survey showed unjustified half-days absent in the year 1 to 6 age group had risen from 16,678 in 2014.
Mrs Smith said she believed that increase also reflected a more accurate collection of data and stricter protocols for determining what was classified as unjustified and justified absenteeism.
In the past, schools had greater flexibility in granting justified status to an absent pupil, but the systems for collecting data were now more rigid.
"It’s not a good trend," she said.
"Attendance is absolutely paramount.
"It definitely makes a difference. Regular and consistent attendance at school is imperative for learning outcomes."
Another troubling trend was the increase in families taking children out of school to go on holiday during the term.
She believed that had increased the number of unjustified absences.
"It never used to be acceptable."
Ms Casey said families took their children out of school for a variety of reasons.
"We define unjustified absence to include situations where the student is not at school and the reason is unknown or the explanation given doesn’t fit the school’s policy as a justifiable reason to take the student out of school, even though the parents may consider the absence was justified and may have provided a written explanation," she said.
She said examples were when a pupil stayed at home to look after another family member, a family holiday or when the child had a test and was not ready.
