Overall truancy in England's secondary schools decreased last autumn then worsened in spring, new figures show.
New more detailed breakdown picks out "absence" due to lateness
A minister urged parents not to take children on holiday during term, as more than 5.4 million days were lost for that reason in all schools.
The absence statistics are now being reported by schools on a termly basis.
Those for autumn 2006 and spring 2007 showed a worsening picture in academies, with unauthorised absence almost double that of other schools.
A spokesman for the Department for Children, Schools and Families said newer academies often inherited serious absenteeism problems that took time to put right.
"What we do know, however, is that many older academies have successfully turned this around over several years."
In autumn 2006 unauthorised absence in other secondary schools was running at 1.35% of the half-day sessions pupils should have attended, against 1.34% the previous year.
Overall absence however was 7.26% against 7.45% in 2005.
But in academies, reported separately, overall absence rose from 8.52% to 8.79% and unauthorised absence rose from 2.21% to 3.03%.
In the spring term overall absence in secondary schools fell again from 8.99% in 2006 to 8.38% this year, but unauthorised absence rose from 1.49% to 1.61%.
In academies, overall absence rose from 9.98% to 10.34 and unauthorised absence from 2.62% to 3.04%.
The publication stresses that the academy figures are not "like for like" because there were 27 open in 2005-06 and 46 in 2006-07.
The government said research conducted for the Local Government Association had found that academies had higher proportions of pupils eligible for free school meals than in the local area generally, more pupils with special educational needs and more with lower prior attainment.
Other recent figures have shown that academies expel pupils at twice the rate of other schools.
Children's Minister Kevin Brennan said the rises in unauthorised absence reflected the tougher approach schools were taking to reporting the matter.
Shadow Schools Minister Nick Gibb said the government seemed to be "in denial".
"The inexorable rise in unauthorised absences in secondary schools is yet another sign of problems with discipline and behaviour in our education system that remains unresolved despite nearly a billion pounds of public money and a range of government initiatives."
Behaviour had to be improved, he said.
"We also need to ensure that children are set by ability, stretching the most able and giving the less able the time and space to learn.
"This reduces boredom and disaffection and lessens the likelihood of a child truanting from school."
Liberal Democrat schools spokesman David Laws said: "These figures hide the reality of thousands of children who have fallen out of the education system and who are hanging around on our streets instead of developing the skills they will need.
"We need not only tougher school discipline but a curriculum which is relevant
for students of differing interests and abilities."
There were no previous year figures for primary schools, but unauthorised absences rose from 0.48% in the autumn to 0.57% this spring.
Cost of holidays
Of the total days lost due to holidays, 530,000 had not been authorised by the schools though in the vast majority of cases schools had agreed to the children's absences.
Schools can grant up to 10 days authorised holiday per year, though official guidance to head teachers says this should not be an automatic right for parents.
Mr Brennan said: "While it's fair that heads should have the discretion to allow parents up to a fortnight for holidays in exceptional circumstances, local authorities should not tolerate instances where parents wilfully take their child out of school without authorisation."
He added: "Travel companies have a role to play in keeping prices competitive during school holidays."
Agreed family holidays accounted for 12% of the reasons for absence (17% in primary schools and 8% in secondaries).
The figures 53% were because of illness, with a further 7% for medical appointments.
Arriving late accounted for just over 1% of unauthorised absences.