Exam marks in more than 10 per cent of A-levels, sat by tens of thousands of pupils, were "artificially" devalued in order to restrict the numbers gaining the new A* grade, it has emerged.
Heads fear this means some of the brightest pupils being unfairly downgraded and denied scarce university places.
While exam regulator Ofqual said initially that the controversial measure would only be used in "exceptional" circumstances, its own figures now show that the value of some marks was changed in 33 of the 214 summer A- level awards as part of an effort to keep the numbers of A* grades within expectations.
In 23 of those cases, it led to the value of pupils' marks being reduced so that fewer candidates received A* grades than would otherwise have been the case. In the remaining 10 cases, the value of marks was increased to boost the number of pupils getting A*s.
A total of 83,078 candidates sat 14 A-level subjects in England where the value of marks was reduced.
The exam boards stressed that any concerned schools could make enquiries through the normal channels, but insisted that the A* grades awarded were "a fair representation of those candidates who achieved at the highest level".
Ofqual statistical guidelines, based on last year's results, suggested that 7 per cent of grades should be A*s but the final proportion was 8.1 per cent.
Isabel Nisbet, Ofqual chief executive, said: "I am in no way complacent as a regulator, but I think it has been a very secure technical exercise."
The regulator instructed exam boards to refer to statistical guidelines when deciding where grade boundaries should lie, so it could ensure that standards remained constant in a year of big changes.
Meanwhile, the pass rate for GCSE has risen for the 23rd year in a row: 69.1 per cent of entries gained at least a C, a rise of 2 per cent. Record numbers got top grades, with 22 per cent awarded AA* grades, and around one in 10 pupils took English and maths a year early.
The gap between the top grades achieved by Welsh pupils and those in the rest of the UK has widened for the fourth year in a row - 66.4 per cent got A*-C grades, 2.7 per cent below the overall figure.
33 of 214 summer A-levels had marks changed to stay within A* expectations.