Just over 5% of secondary school children are 'persistent absentees'
The overall truancy rate in England's schools increased slightly last year to a record 1.01% of half-day sessions.
Unauthorised absence in primary schools was up from 0.52% to 0.57%. It fell in secondaries from 1.52% to 1.49%.
The rate of "persistent absence" - of those typically missing a fifth of lessons, both with and without permission - fell from 4.1% to 3.6%.
The government says the figures show that its focus on this group of pupils is the right approach.
But these youngsters - one in 20 secondary pupils - missed 35% of their schooling during the last year.
Almost a quarter of a million pupils were classed as "persistent absentees" this year.
The rate is much higher among pupils eligible for free school meals, and there are a slightly more boys in this category than girls.
These pupils are responsible for just under a quarter of all unauthorised absence in primary schools, and 15% in secondary schools.
But the percentage of secondary pupils missing school without permission is markedly higher than 10 years ago - up from 1.01% of half-day sessions missed in 1997 to 1.49% in 2007-2008.
Over 5% of all enrolments in secondary schools are classed as persistent absentees. In special schools, the rate is over 10%.
In English primary schools, rates of absence appear to be rising - from 0.43% in 2004 to 0.57% this year.
The overall absence rate - including both unauthorised and authorised absences in all types of schools - is 6.29%.
The Department for Children, Schools and Families calculates the number of half-day sessions missed to arrive at the percentages.
In Academies, government-funded schools run by outside benefactors, rates of absence are higher but have fallen by 15 percentage points.
The Tories said the government needed to focus on tackling increasing truancy in primary schools.
Conservative shadow schools secretary, Michael Gove, said: "We know that persistent absenteeism and truancy is linked with low levels of literacy. Tackling the epidemic of reading failure early in primary school is crucial."
But the minister for children and young people, Delyth Morgan, said the government's drive to reduce absence, particularly persistent absence, was proving successful.
"Making sure a child attends school is also down to parents not providing excuses for their child's absence.
"Schools and local authorities are providing support to parents and penalising those parents who regularly flout this responsibility by using the range of measures available to them, such as parenting contracts."
The new statistics relate to England. The most recent data for Wales show 1.8% of half-day sessions missed through unauthorised absence in secondary schools in 2007-08 and 0.9% in primaries in 2006-07.
In Scotland, the quality and consistency of the recording of the reasons for absence by schools is regarded as so poor that unauthorised absence is no longer counted.
The overall absence rate in 2007-08 was given as 6.8%.