Around 20,000 Northern Ireland school pupils missed almost six weeks' worth of lessons in one year.
The unauthorised absence rate is now double that in England, the Northern Ireland Audit Office said.
Those in greater deprivation and entitled to free school meals, in state care or from traveller families were most likely to skip classes, the public spending watchdog said.
Students not attending grammars also had higher non-attendance levels.
Fewer than 4,000 of the affected pupils were referred for special support in 2011/12 despite high levels of non-attendance.
Auditor Kieran Donnelly said: "Regular school attendance and educational attainment are inextricably linked.
"It is therefore disturbing that around 20,000 pupils missed more than 15% of their lessons in 2011-12."
This equates to six weeks of schooling.
Persistent absentees are more likely to underachieve in exams and seven times more likely to not be in education, employment or training by age 16, the Northern Ireland Audit Office (NIAO) said.
The report's main findings included:
- In 2011-12 pupils whose absence was recorded as unauthorised missed around £22 million worth of education.
- Since the last time the Audit Office reported, in 2004, the Department of Education has made some progress on data collection, commissioned research into improving attendance and issued policy documents and guidance.
Overall attendance levels have improved marginally from 93.6% in 2007-08 to 94.2% in 2011-12. The 2011-12 absence equated to around nine days missed per pupil at primary school and 13 at post-primaries.
However the level of unauthorised absence has increased, accounting for a third of all absences.
Traveller children missed up to 40% of the school year while rates of absence were notably higher for children in care attending post-primaries.
More than 80% of persistent absenteeism was not referred to the Education Welfare Service for special support.
Some schools achieved good or improving levels of attendance despite challenging circumstances. They intervened early, effectively used attendance data and engaged with parents and the wider community.
The public spending watchdog said: "Although pupil attendance has improved since statistics were first collected in 2007-8, levels of unauthorised absence remain a challenge and a number of disparities in attendance rates persist across several groups of pupils.
"Given that 16,000 cases of persistent absence were not referred to the Education Welfare Service in 2011-12, there is a risk that disengaged pupils could be failed by the system.
"It is vital that all our children attend school regularly and make the most of the opportunities that the education system offers to them.
"This will not only improve the life chances of our young people but will also ensure that our economy is well-equipped to compete in an increasingly global marketplace."
The report made 14 recommendations. It said schools in deprived areas should share information and good practice.
- Schools should use attendance statistics during monitoring of a pupil's overall performance throughout their time in compulsory education and should discuss them at parent/teacher meetings.
- Schools should refer all cases to the Education Welfare Service where intervention is deemed necessary.
- The Department of Education and education and library boards should work together to identify and offer support to schools with high levels of unauthorised absence and a high concentration of vulnerable pupils.