More than 10,000 pupils were absent from high schools for more than 25 days in 2015-16, the equivalent of five weeks off.
Meanwhile nearly 15,000 of students in Wales had no days off at all last year - the highest recorded.
Overall absence levels in secondary schools were down to their lowest level since 2006-07.
But the number of secondary and middle school pupils going on unauthorised holidays during term-time has increased.
In Wales families are allowed up to 10 days of term-time holiday at the head's discretion.
Last year 3.6% of all absences were because of holidays that had not been agreed by schools - an increase from 3.0% in 2014-15.
Education secretary Kirsty Williams said the falling absence rates were a "testament to the dedication" of teachers, parents and councils.
She said: "I am really pleased to see levels of overall absenteeism in secondary schools continue to fall and now stand at their lowest level for 10 years.
"This is testament to the commitment and dedication of parents, teachers, and local authorities across Wales who are helping our young people understand that if they are going to fulfil their potential, regular school attendance is vital."
Sickness remains the main reason 11 to 16-year-olds take time off school, accounting for 60.7% of all absences.
Meanwhile the proportion of absence due to family holidays agreed by the school fell from 5.9% in 2011-12 to 1.8% in 2015-16.
Earlier this year then education minister Huw Lewis wrote to councils to say it was wrong to tell head teachers to ban all term-time leave.
His intervention followed a petition by parents last year against fines for taking holidays in term-time.
South East Wales had the highest number of 11-16-year-olds missing school classes last year, while North Wales had the lowest.
Newport recorded the highest absence rate with children missing 6.8% half school days, while Gwynedd and the Vale of Glamorgan had the lowest rate at 5.0%.
Flintshire had the lowest rate of unauthorised absence at 0.4%, with Newport recording the highest at 2.1%.
The Wales-wide unauthorised absence rate has remained static at 1.3% for the last few years.
Figures show Wrexham, Flintshire, Powys, Pembrokeshire, Swansea, Neath Port Talbot, Rhondda Cynon Taf, Merthyr Tydfil and Monmouthshire all saw slight increases in the unauthorised absences last year,
The figures also show pupils eligible for free school meals were more likely to miss classes, while girls were more likely to miss school than boys.

Two footballers apologised after being photographed apparently urinating into a glass at last year's festival, where women were seen baring their breasts.
Chief executive Ian Renton said: "It's to ensure that drinking is not the rationale for people coming racing."
The measure is also to be imposed at the Jockey Club's other racecourses.
It comes in first at Cheltenham, where the festival takes place next month, but will be in place at Epsom, which stages the Derby, and Aintree, where the Grand National is held.
"It's an improvement on things we are already doing," Mr Renton said.
"Aintree has already got the ball rolling, with their Ladies' Day, they've already taken steps to improve the way that is perceived.
"We want them to come to racing and enjoy the sport and not have those people coming who will be a nuisance to other racegoers," added Mr Renton.
As well as the four-drink limit, corporate complimentary bars will close earlier and water points will be made available in every public bar.
The number of children missing school in Wales has fallen to an all time low, government statistics have shown.
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Cheltenham Festival racegoers will be restricted to buying four alcoholic drinks at a time in a bid to crack down on anti-social antics.