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Figures show the number of candidates achieving five A* to C grade passes dropped by 0.4 percentage points to 69.4 per cent – the first time the figure had fallen since the exam was first sat in 1988.
In addition, the proportion obtaining A* or A grade passes also fell from 23.2 per cent to 22.4 per cent.
The drop follows a similar fall at A-level last week at a time when exam boards face pressure from both Education Secretary Michael Gove and Ofqual, the exams regulator, to end grade inflation.
Exam boards said the main reason for the decline was the introduction of a new tougher syllabus for GCSE science, which saw A* to C grades drop by 2.2 percentage points to 60.7 per cent.
However, the most fury was reserved for a drop in the English pass rate, for which heads and teachers blamed the exam board for switching the boundary for a C grade pass by as much as 10 marks (64 instead of 54 out of 100).
The change will mean thousands of students are likely to miss out on sixth-form or college places, and it could also lead to the closure of scores of schools for under-performing.
"It is morally wrong to manipulate exam grades in this way – you are playing with young people's futures," said Brian Lightman, general secretary of the Association of School and College Leaders. "Students who were working at a C level throughout the year who were told on their assessments they were in line for a C have found out today that this is worth a D. This means they may not get their places at college or sixth-form.
"Failure to gain a C or above in English blocks access to post-16 study and many career paths. It could also demoralise students who are at the highest risk of dropping out."
Mike Griffiths, head of Northampton School for Boys, said his school had seen a 12 per cent drop in the number expected to get A* to C grade passes in English. "It's not the teachers," he said. "Every one of the teachers has been at the school six or seven years and regularly get between 85 and 90 per cent C's and above.
"It has been impossible to get out of the exam boards exactly what the grade boundaries should be.
"We need to look at the whole thing carefully and perhaps carry out an inquiry to find out what happened.
"I just hope Ofsted doesn't come in with their clodhoppers to the schools where results have fallen. They have to be wary about drawing conclusions."
Last night Mr Gove denied there had been any political interference saying: "The decision about where to set grade boundaries is made by exam boards.
"If you take English, then 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 the result of the independent judgements made by exam boards free from any political pressure."
Exam boards admitted they had changed the grade boundaries in some English GCSE units and other subjects. They pointed out that candidates in maths, English and science were sitting new syllabi for the first time.
The changes are understood to have been made after it emerged that those sitting the exam early in winter were getting higher grades than expected.
The boards have been told by Ofqual, the exams regulator, they should curb grade inflation and keep the pass rate at roughly the same as last year. Education Secretary Michael Gove has also said he wants an end to grade inflation and "dumbing down" of exams.
However, the upshot is likely to be that fewer schools than expected will reach the Government's new "floor target" of 40 per cent of pupils getting five A* to C grades including maths and English, up from 35 per cent last year. A total of 107 schools failed to reach it last year but this could double with schools in the firing line being forced to accept academy status and their heads being fired.
Exam boards are bracing themselves for challenges from disgruntled pupils and schools over their grade marks.
Meanwhile, yesterday's results also saw an increase in the overall pass rate from 98.8 per cent to 99 per cent. Overall, 658,000 16-year-olds sat the exams. Girls outperformed boys at every level – in contrast to A-levels last week where boys obtained more A* grade passes. In all, 8.7 per cent of girls gained an A* compared with 6 per cent of boys.
Schools Minister Nick Gibb said: "Tens of thousands of people are today reaping the rewards of their hard work over the last two years... They can all be proud of their efforts."
John Cridland, director general of the CBI, said: "Enhancing the rigour of our examination system will help to improve our examination system compared with our international competitors."
Languages: More students choose to speak another tongue
The first boost in the take-up of modern foreign languages, after more than a decade of decline, was revealed in yesterday's GCSE results, writes Richard Garner.
Figures showed a significant increase in Spanish – up 10 per cent to 66,021 and established as the second most popular language taught in schools.
In addition, there were increases in the take-up of the "newer" foreign languages such as Mandarin, where numbers rose by 19 per cent and growing numbers of non-native Chinese speakers sat the exam.
French and German still fell – but by less than previous years –French was down by 0.5 per cent to 153, 436 and German by 5.5 per cent to 57, 547.
Overall, there was a 0.9 per cent rise in the take-up of the subject – the first since languages no longer became compulsory for 14 to 16s six years ago.
Exam boards put the rise down to Education Secretary Michael Gove's decision to introduce the English Baccalaureate – to be awarded to pupils who obtain five A* to C grade passes in English, maths, science, languages and a humanities subject – either history or geography.
History and geography showed a revival, too, up 2 per cent and 3.5 per cent respectively, following falls of 1.2 per cent and 7.1 per cent the previous year.
Performance: 'Bog-standard' school's results a class apart
Stretford High School in Trafford, Greater Manchester, could be thought of as a "bog-standard comprehensive" – to use the words of former Labour spin doctor Alastair Campbell.
But yesterday the community comprehensive sent out a powerful message on behalf of local-authority schools by recording a dramatic improvement in the GCSE results of its most disadvantaged pupils – cutting the gap in performance between those on free school meals and their more affluent classmates from 19 per cent to just 4 per cent.
It also bucked the national trend by securing a four-percentage-point improvement in A*- and A-grade passes – and similar improvements in maths, too, with 66 per cent of students getting at least a C-grade pass.
According to James Haseldine, the head teacher, the secret of its success lies in tracking pupils closely throughout their schooling.
As soon as they show signs of failing to reach targets, an individual plan is drawn up to improve their performance.
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