Schools across the country are preparing to order wholesale remarking of test papers following a sudden slump in the proportion of entries marked A* to C - the first annual drop in the exam’s 24-year history.
Most complaints surrounded GCSE English where grade boundaries appear to have been dramatically raised compared with previous assesments.
In one "controlled assesment" task set by the Assessment and Qualifications Alliance in January, pupils needed just 54 per cent to gain a C grade. But pupils taking a similar assesment in June needed to secure 66 per cent for the same mark.
C grade boundaries increased in many other AQA English papers and some English assesments set by Edexcel. One C grade pass rate increased from 57 to 67 per cent.
It came amid an overall decline in the number of pupils gaining good grades. Some 63.9 per cent of test papers set this summer were awarded at least a C compared with 65.4 per cent in 2011.
On Thursday, examiners admitted grade boundaries had been changed in some subjects but denied that results had been deliberately depressed in English.
But a Government source suggested that grade boundaries set for the January exams had been too low – resulting in a sudden raising of requirements to counter severe grade inflation.
It was also claimed that a fall in results reflected an increase in the number of pupils sitting tests in the summer – instead of winter – and the introduction of new combined English language and literature GCSE papers for the first time this year.
But the move sparked a storm of protest.
The Association of Directors of Children’s Services, which represents local authority chiefs, called on the Department for Education to launch an official investigation into the drop.
Labour questioned whether Ofqual, the exams regulator, had put pressure on individual exam boards to “shift grade boundaries”.
Michael Gove, the Education Secretary, said the decision to change the grade boundaries was down to individual exam boards.
He said: "You cannot have a situation where exam passes continue rising forever and ever without there being in some subjects at some points grades either falling or steadying or changing - it's just in the nature of things that inevitably there will be alterations."
"That is a result of the independent judgments made by exam boards entirely free from any political pressure and I think that the various chief executives of the exam boards, and indeed the chief executive of the regulator Ofqual, have made it clear today that these decisions have been made because the exam boards and the regulator have sought to ensure this year as every year, that exam results are comparable over time so that we can all have confidence in the examination system."
Conservative-controlled Westminster Council said it “appears the goalposts have been moved for a particular group of children halfway through their two-year exam, which is simply not fair”.
Last night, examiners were preparing for a surge in the number of re-mark demands amid fears a fall in headline grades may lead to pupils missing out on sixth-form college places.
St Aidan's Church of England Academy in Darlington said it expected results to exceed last summer, when 44 per cent of pupils gained five good grades, including English and maths. But on Thursday it emerged that just 34 per cent of students had hit the mark.
Alison Appleyard, the principal, said: "I simply don't believe the English marks are correct. We have asked the examining board to review the situation with all urgency.
"We hope that this will be rectified very soon.”
Results at four out of five schools run by ARK– one of the biggest backers of the Government’s flagship academies programme – were down this year.
Lucy Heller, managing director, said: “While the movement in the GCSE English threshold has hit overall attainment levels in the short term, all our schools are committed to raising the bar higher in this and other subjects.”
It was claimed that around 30 students from St Mary's Catholic High school in Astley, Greater Manchester, received D grades when Cs were predicted.
Janet Parkinson, head of English, said: “They have raised the bar that's needed to get a grade C. They have done it, I think, as a political move and it's very unfortunate for students who are in this year's crop."
Many schools refused to submit grades to The Daily Telegraph’s annual GCSE results because of complaints marks were too low.
Brian Lightman, general secretary of the Association of School and College Leaders, said: “What appears to have happened is that, halfway through the year, it was decided that too many students were going to get a C grade in English and the grade boundaries of the exam were pushed up very substantially.
“It is morally wrong to manipulate exam grades in this way – you are playing with young people’s futures. Failure to gain a C or above in English blocks access to post-16 study and many career paths.”
But an Edexcel spokesman said: "Our changes are comparable to those of other awarding organisations. For English we made changes to grade boundaries in the range of two to 10 marks. This needs to be taken in the context of the fact that Edexcel units have more than double the marks available compared those of other boards.
"We only made changes to three of nine grade boundaries."
An AQA spokeswoman said: "This summer, all the exam boards raised their grade boundaries for GCSE English in order to maintain standards. In AQA's case, this was by between zero and three marks.
"We take account of how students have performed in each exam series when we set grade boundaries, in order to ensure that standards are maintained. While grade boundaries can therefore vary between exam series, students can be confident that the grade they get for an overall qualification one year would be the same the next."
Ziggy Liaquat, managing director of Edexcel, said: "We do understand that students and teachers not getting results they anticipated is unsettling.
"But I think the key point is we base our decisions on the quality of the work that we see in front of us. We use other data points to do this in collaboration with the regulator, so at qualification level, students should be reassured that they've got the grade that their work merits."