Newly released internal e-mails have disclosed that, in August last year, exam standards regulator Ofqual was given predictions of a big jump in science results.
On August 10, just two days before the grades were finalised, Ofqual chief executive Isabel Nisbet wrote to exam board officials saying the anticipated increases would be "difficult for the regulators to justify and for all of us to defend." It was then agreed the independent awarding bodies that set and mark papers should "change their grade boundaries in order to improve the national position".
The general secretary of the Association of School and College Leaders, John Dunford, said: "I am shocked. Grades should not be altered on the basis of statistics, but on the basis of standards."
Fears have now been raised that thousands of pupils may have missed out on the grades to which they were entitled.
Ofqual chief executive Isabel Nisbet argued that most candidates already had results from previous exam units, so the fix would have only had "a very small effect" – but critics say pupils could have missed out on the A* and A grades that are essential for entry to university.
The number of pupils gaining grade C and above, meanwhile, is essential for a school's positioning in the league tables.
The chief executive of the OCR exam board, Greg Watson, said: "It's important exam standards are regulated effectively, but in GCSE science, Ofqual intervened too late, in haste and over-simplistically."
The internal e-mail sent by Ms Nisbet on August 10 read: "In science, the table showed an increase of 2.42 percentage points in the proportion of candidates expected to get a grade C or above in GCSE science, compared with the actual figure for 2008; and an increase of 0.83 points at grade A.
"We agreed that increases of these magnitudes would be difficult for the regulators to justify and for all of us to defend."
The eventual results, released on August 29, showed an increase of 0.9 per cent in the proportion of pupils gaining C and above and an increase of 0.2 per cent in A* or A grades.
A spokesman for Ofqual, the independent body set up by Schools Secretary Ed Balls, said: "In our work to regulate the awarding of the 2009 GCSE science exams, our aim was to ensure that awarding bodies set the right standards and candidates got the grades their work deserved.
"It is our expectation that the differences between the awarding bodies will be significantly reduced in 2010."
The headmistress of Lady Eleanor Holles school in west London and president of the Girls Schools Association, Gillian Low, said: "If these students genuinely deserved grades they didn't get, it's quite scandalous."
Tory Shadow Schools Secretary, Michael Gove added: "It is deeply worrying that the bureaucrats who should be guardians of academic rigour seem more worried about presentation than education."
Criticism of GCSE standards has been growing since new exams were first taken in 2008.