The three-year research project looked at 454 schools and found a hard core of truants - one pupil in 50 - was responsible for almost half the days missed. One in 100 were absent for half a term or more, with more than 600 missing at least a third of the school year.
In addition, a quarter of pupils truanted for up to one week a year and one in 20 for between one and two weeks, the study conducted by the National Foundation for Educational Research for the Department for Education and Skills found. Sixty-five per cent had no recorded unauthorised absence.
The Government has introduced a range of measures to tackle the problem, including jailing parents of persistent truants.
But it failed to hit its scaled-down target of cutting truancy by 10 per cent by 2004. The original target was to reduce it by a third.
David Cameron, shadow education secretary, said: "Sadly, these figures come as no surprise. Despite having spent more than pound;800 million on truancy initiatives since coming to power, this government has failed to get any real grip on the problem. It claims to take truancy seriously, but as yet has very little to show for it."
Pupils absent from schools for long periods, whether as a result of truancy or for a legitimate reason such as illness, achieved lower exam results than their peers.
The report said: "At key stage 4, where periods of total absence exceeded three weeks, a young person's probability of achieving five or more A* to C grades was reduced by 18 per cent, while their probability of achieving no grades above a C increased by one third.
"Periods of absence above five weeks decreased a pupil's probability of achieving five or more A* to C grades by one third; it increased the probability of achieving no higher grade GCSEs by more than 80 per cent."
The impact of lost lessons is greater on boys and low-attaining pupils, it said.
A DfES spokeswoman said: "School attendance is at record levels but we want to see further improvement. In the spring term alone, attendance in secondary schools improved, with an extra 3,000 pupils attending school each day compared to last year."
An analysis of pupil attendance data in excellence in cities areas and non-EIC EAZs: Final report by Marian Morris and Simon Rutt, National Foundation for Educational Research is available from www.dfes.gov.ukresearch