The statistics, from Northern Ireland Statistics and Research Agency, highlight that post-primary attendance in Belfast's Blackstaff and Coole in Newtownabbey are around the lowest in the region.
Both are majority Protestant areas and Alan Logan, Principal of Belfast Boys' Model Schools said they have introduced strategies to tackle absenteeism.
"Where issues do arise form teachers will contact parents and talk to parents if there would appear to be some issue arising, and we would also involve a counsellor, perhaps if a boy would appear to be experiencing some difficulty or some reason why he was reluctant to come to school.
"The relationship with parents is key, I believe, in improving attendance," Mr Logan told UTV.
But Ulster Unionist MLA Roy Beggs, who uncovered the figures, said although many schools have taken action, everybody should be concerned.
"I've come across areas where schools appear to be doing everything right, the school itself has excellent monitoring systems looking after attendance, texting parents is producing good results itself, but yet adjacent to the school there might be areas where, for some reason, the community has not been valuing education the way it should, and there are still high pockets of deprivation with high levels of young people not attending school," the East Antrim Assembly member added.
Professor Pete Shirlow from Queen's University, Belfast said the problem within Protestant working class areas is a legacy of industrialisation.
It's the loss of a type of life that was in the Protestant working class community where we had apprenticeships.
Prof Pete Shirlow
"I think it's also the nature of those communities where many of the people who were capable have left, and left behind a population which maybe does not function as well as it could," he explained.
Mr Beggs also said the figures are a throwback to the days of Harland and Wolff, when people left school to pick up a trade.
"That's decades ago and for some reason the community has not to the importance of education," he commented.
Figures also show that a Catholic child with free school meals is twice as likely to go to university as a Protestant child with free school meals.
"Both are living in poverty, both are experiencing the same social exclusion and one is twice as likely to go to university as the other. That tells us that there's something fundamentally wrong," added Prof Shirlow.
But Mr Logan said he believes views in the working class Protestant community are changing.
"Perhaps historically there has been a view that education isn't perhaps all that valuable. Perhaps there has been, in some families, a lack of vocational aspiration, but I would say I see very definite sense of that changing. We've taken a number of steps to engaging parents in learning and in the life of the school," he explained.
Where Prof Shirlow believes Catholic education "created a sense of achievement, a sense of community attitude towards education", he said the same needs to be done with Protestant education, adding, "We need to see someone within unionism who's prepared to take the lead with this."
"We need all public bodies working closely with the voluntary and community sector to address poor attendance in school and the corresponding educational underachieving," added Mr Beggs.
"We need everyone to value education and recognise that whilst education cannot guarantee a job, it will improve the likelihood of finding employment.
"We as a community need to do more for all our young people and ensure that there's opportunity for everyone."