Up to one in seven students who gains A grades at A-level only does so by re sitting easier AS papers, The TES can reveal.
And the Qualifications and Curriculum Authority has ducked action to curb the retakes culture amid fears that it would harm a government drive to raise student numbers in maths, science and languages.
The findings come as the Government tries to take the politics out of regulation by making part of the QCA independent of ministers.
The restructured watchdog will face further challenges to cope with an increasingly divided qualifications system. A survey by the Headmasters' and Headmistresses' Conference suggests that nine out of 10 of England's top independent schools have abandoned GCSEs in at least one subject to do the international GCSE, a more traditional version of the exam.
The QCA's report on re-sits shows the proportion of students achieving As in AQA's physics A-level would be cut from 31.2 to 26.6 per cent if only AS papers taken by the end of Year 12 counted. Instead, students are using retakes in their final year, after AS courses have finished, to enhance their overall grade.
An analysis of AQA psychology results showed that A grades would fall from 20 per cent to 17.5 per cent if re-sits in Year 13 were ruled out. For AQA English literature, the reduction was from 24 per cent to 21.5 per cent. The QCA report said most teachers surveyed in 32 schools and colleges wanted students to be offered just one re-sit.
But the authority rejected this. Minutes of a QCA board meeting show it was concerned that it would hit maths, science and languages hardest, "where the Government is keen to see entries rise".
Re-sits in Year 13 may help to explain much of the recent increase in A-level A grades.
This year, 25.3 per cent of A-level entries were awarded an A. If AS re-sits in Y13 were banned and retake patterns for all exams were the same as in AQA physics, the national A-grade rate would be cut to 21.6 per cent. This is not much of an improvement on the 19.1 per cent registered in 2001 before the current retake rules were introduced.
Kevin Stannard, who has led the development of an alternative to A-levels, the Cambridge Pre-U, said: "We have been told consistently by universities that they were having difficulties with candidates appearing with a grade and not knowing how they got it, how many times they had to re-sit a unit."
Under plans announced by Ed Balls, Children, Schools and Families Secretary, at the Labour party conference in Bournemouth, the QCA is to be split. Its regulatory division will be turned into a new body to report to Parliament.
Mr Balls said the changes would help to end the "sterile debate" over whether GCSE and A-level standards are being maintained. Teachers' union leaders welcomed the move as a step in the right direction, but government observers were unconvinced that the standards debate would go away.
QCA restructured, pages 4-5
A-star elitism, pages 14-15