Seven per cent of pupils "unlearn" reading, maths and language skills in their first secondary year and their marks drop by up to a third in standardised tests compared with their last primary year, the study by Professor Maurice Galton of Homerton College, Cambridge, found.
Up to 40 per cent of all 11-year-olds are still failing to make satisfactory progress during their first year of secondary school because existing programmes place too much emphasis on the social, rather than academic, effects of transfer, the study found.
However, many children become disenchanted with learning as they progress within the same school and find it hard to lose a reputation as a "dosser" and become a "worker".
Pupil motivation and performance dropped dramatically between Years 7 and 8 as the novelty of the move to "big school" wears off, researchers found.
But progress also dipped for eight and nine-year-olds as they were turned off learning by the transition from infants to juniors.
Children who transfer to middle schools at the end of Year 4 showed the biggest skill loss, with one in eight pupils showing a major drop in test scores.
Curriculum continuity was still a problem despite the introduction of the national curriculum, researchers reported. Pupils particularly lost interest in science and technology at secondary school, partly because induction day demonstrations featuring loud bangs and exciting displays had given them unreasonably high expectations.
Only one in three pupils were found to be fully focused during secondary science lessons, compared to 60 per cent at primary school. Only half of secondary pupils concentrated throughout maths lessons, down from 61 per cent in primary lessons.
In English the use of classroom assistants to help pupils with reading difficulties was believed to have held children's interest - the percentage of "fully engaged" pupils fell only slightly from 64 per cent to 61 per cent.
Most of the initiatives to help children transfer from primary to secondary school have concentrated on the social effects at the expense of evaluating the impact on their academic progress, Professor Galton reported.
A survey of 215 schools found that when schools exchanged information on pupil transfer it was twice as likely to be about administrative or pastoral matters than about the curriculum. Only one in three respondents had confidence in the information that they sent to other schools. Even fewer - 26 per cent - had confidence in information received.
He concluded that schools need to be provided with an array of tried and evaluated strategies which can be adapted for their particular circumstances and that more research is needed into how to help pupils at transfer.
Professor Galton's report said: "Pupils in secondary schools frequently see the years between national key stage tests and public examinations as somehow less important and do not appreciate that working hard during these periods can have pay-offs later.
"They can become preoccupied with friendships and gain a reputation for messing around; pupils who want to change from being a dosser to a worker find it extremely difficult to shake off their old image. Consequently, they may decide to give up rather than to catch up."