The "Attendance in New Zealand Schools 2011" report shows an average of 2580 pupils were absent from school in Otago during the week-long survey, which took place from June 13-17.
Of those absent during the week, 668 pupils provided unacceptable excuses for their absence. More than half of those were from Dunedin schools.
The figures contributed to the 30,507 unjustified absences nationwide during the survey week.
A breakdown of the statistics showed the highest rate of unjustified absenteeism was among year-13 pupils, and pupils of Maori and Pacific Island descent were most likely to miss classes.
Otago Secondary Principals' Association president Brent Russell believed one of the main causes of unjustified absenteeism was that pupils were disengaged from the system. Many senior pupils who achieved NCEA level 2 or 3 early in the year tended to lose interest in accumulating further credits, and began focusing on post-secondary school activities, such as university study or finding a job, he said.
Mr Russell also queried the timing of the survey, saying the data was collected at a time of the year when mid-winter illness was near its peak.
The percentage of Otago pupils absent from school was well below the 2011 national average. Only 2.2% of the Otago school roll was unjustifiably absent, compared with 4% of the national roll, the report showed.
The report also showed the absentee rate had dropped nationally since the last report in 2009 - a trend followed by schools in Otago.
In 2009, nearly 2500 pupils were absent during the week-long survey, and 813 were unjustifiably absent.
More than 2170 schools participated in the 2011 survey, in which absence data was collected for each pupil for each day of the week.
The rate for each absence type (justified, unjustified and intermittent unjustified) was calculated based on the total school rolls for the participating schools and relates to an average (mean) daily absence for the week per 100 pupils.
The report noted the data did not indicate whether it was the same pupils that were absent or whether different pupils were involved each day.
While the high number of pupils skipping school was unsatisfactory, Mr Russell said it was pleasing to see there had been an overall decline in absenteeism in Otago during the past three years. He credited it to schools' greater use of technology.
"A lot of schools have different systems in place to find out why a child is absent. Some systems are more rigorous than others.
"The good news is, the use of technology is ensuring that schools and/or parents are able to be aware if their kids are not at school."
He said systems which allowed schools and parents to keep better track of their children often discouraged pupils from skipping school.
