Teachers who accused exam boards of marking some GCSE papers too harshly have called for an inquiry into the matter after pass rates fell for the first time in more than two decades.
A number of schools suggested that grade boundaries in this summer's English exams had been substantially increased, with many reporting a drop in the number of children scoring a C or above in the key subject.
It came as yesterday's national results revealed that 69.4% of all GCSE exams were given at least a C grade - down 0.4 percentage points on last summer. It is the first time the A*-C pass rate has fallen in the 24-year history of GCSEs.
GCSE results have falled for the first time in history amid a row over "shifting the goal posts"
Angry headteachers claimed that exam boards had raised English grade boundaries halfway through the year amid fears that too many children were going to get a C.
Brian Lightman, general secretary of the Association of School and College Leaders, accused the Government of yearly "tinkering" and called for an investigation into the issue.
He said: "What has happened this year is not that the exams or standards have been made more rigorous in a way that young people and teachers can prepare for.
"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.
"Standards in schools have not changed one iota. It is the grading that has changed."
He added: "It is morally wrong to manipulate exam grades in this way - you are playing with young people's futures."
Labour echoed the calls for an investigation, saying the Commons Education Committee should carry out an inquiry into what happened.
Shadow education secretary Stephen Twigg said Education Secretary Michael Gove needed to take responsibility for the exam system.
"If pupils from the same year group have been marked more harshly if they were entered later, that is patently unfair," Mr Twigg said.
"We need to understand why some pupils' grades have fallen so dramatically."
Mr Gove insisted that any changes in grades were the result of "independent judgments made by exam boards entirely free from any political pressure".
He said the reason some pupils have had poorer results than expected was partly down to a change in the system which meant their exams had been split into units and modules this year.
This year is the first year that grades have been awarded for new GCSE syllabuses in English. Under the changes, children taking these subjects can now sit exams throughout the course rather than at the end.
Asked about concerns that English papers were marked too harshly, Mr Gove told BBC News: "Yes, the number of As and A*s has fallen, but the number of Bs has increased, the number of Cs has fallen and the number of Ds has increased.
"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 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."
Around 650,000 teenagers in England, Wales and Northern Ireland received their results yesterday, with the proportion of entries awarded at least a C in the key subjects of English, maths and science also falling.
The national figures showed that in the English GCSE, 63.9% of entries got at least a C, compared with 65.4% last summer, while 15% were awarded an A or A*, down from 16.8% in 2011.
In English literature, 76.3% of exams were awarded A*-C, compared with 78.4% last year, and 23.2% got at least an A, against 25% in 2011.
Exam chiefs said that the falls in English were partly down to more candidates switching from taking the subject early in the winter exam season.
They said that historically, there had always been significant numbers of re-sits after the winter exams, and that the winter season tended to produce lower results.
As more students move to take their English exam in the summer, this has an impact on results.
Mark Dawe, chief executive of the OCR exam board, said: "Our job is to maintain the standard of a qualification year on year and in English that has been done. The standard and the results overall have been maintained."
In a bid to tackle grade inflation and to ensure results are comparable with previous years, Ofqual told exam boards that they will be asked to justify any results that are widely different to previous years.
The national statistics also revealed:
:: The gap between girls and boys widened at grades A* to C, with 65.4% of boys' entries attaining that level, compared with 73.3% of girls' entries. Last year, 66% of boys' entries achieved A* to C, compared with 73.5% of girls' entries.
:: In maths, 58.4% of entries got at least a C grade, down from 58.8% in 2011, and 15.4% got A*-A, compared with 16.5% last summer;
:: In science, 60.7% got A*-C grades, down from 62.9%, and 9.8% got A*-A, down from 11.6% in 2011.
:: The slump in modern foreign language take-up appears to be slowing - entries for French fell by 0.5%, compared with a 13.2% fall last year, and the entries for German fell by 5.5% compared with a 13.2% fall in 2011.
:: In England alone, 7.3% of GCSE entries were awarded an A* and 69.5% achieved a C or above. Both figures are slightly down from last year's results.