Education Secretary Michael Gove denied political interference in this year's GCSE results, as A*-C grades fell for the first time in the exam's history.
Mr Gove insisted exam boards made their own decisions about where to set grade boundaries, amid claims of last minute changes to English GCSE boundaries.
Head teachers are angry at a drop in the number of pupils who achieved at least a grade C in their English GCSE.
The row broke out as about 658,000 16-year-olds received their results.
Across all subjects, the proportion of GCSE entries in England, Wales and Northern Ireland awarded at least a C has fallen for the first time since the exams replaced O-levels in 1988.
This year's results, published by the Joint Council for Qualifications (JCQ), show 69.4% of all subject entries earned grades A*-C, compared with 69.8% last year.
Pupils receiving A* and A grades were down from 23.2% last year to 22.4%.
But it was the grades awarded in English that appear to have caused the most upset, with teachers saying this summer's papers were marked too harshly.
Individual schools have reported unprecedented numbers of pupils failing to get a grade C or above.
In GCSE English, 63.9% of entries got at least a grade C, compared to 65.4% last summer. Some 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 to 78.4% last year, and 23.2% got at least an A, against 25% in 2011.
Mr Gove told the BBC that exam boards, in conversation with England's exams regulator Ofqual, were ensuring that new style exams, sat for the first time this year, were comparable with those in previous years.
But he stressed: "The decision about where to set grade boundaries is made by exam boards.
"If you take English, then 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.
"And that is the result of the independent judgements made by exam boards entirely free from any political pressure."
He said he had not been expecting a fall in grades, adding that these new GCSEs in maths, English and ICT, had been brought in by the previous Labour government.
Mr Gove, who has spoken of a possible return to more rigorous exams based on the old O-level, said the government would bring forward proposals for the reform of GCSEs to the autumn.
"We want to change them, to improve them."
Shadow Education Secretary Stephen Twigg said it was important to understand why results had fallen.
"Is it because of pressure from Ofqual to shift grade boundaries?
"Serious concerns have been raised regarding the English GCSE in some quarters. As well as ensuring standards remain rigorous, we must ensure all pupils are treated consistently and fairly.
"Michael Gove and his education ministers must explain what has happened."
Brian Lightman, general secretary of the Association of School College Leaders, said the English results must be looked into, saying it was "morally wrong to manipulate exam grades in this way".
He said: "The big issue, schools are telling us, is at the C/D borderline in English.
"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.
"Students who were working at a C level throughout the year, who were told on their assessments that they were in line for a C, have found out today that this is worth a D."
It has also emerged that the Welsh government had concerns about how some English GCSEs were being assessed.
Welsh Education Minister Mr Andrews said: "We had concerns about the methodology being used by Ofqual in relation to English Language GCSE, and my officials raised these with Ofqual two weeks ago.
"There will be further meetings with Ofqual on this in the autumn."
But the exams boards insisted this year's grades were comparable to any other and that examiners were "comfortable" with the grades awarded.
Mr Andrews later said he believed the exam system was being "politicised" in England - and that exam boards had been pressured to mark more harshly.
"When Michael Gove says jump, the head of (exam regulator) Ofqual says 'how high'," he said.
"We need to look at the integrity of the Welsh system and whether we can have confidence in the Welsh system if political decisions in London are going to undermine performance in Wales."
And Cllr Nickie Aiken, Westminster City Council cabinet member for children, young people and community protection said "it appears the goal posts have been moved for a particular group of children halfway through their two-year exam and study period, which is simply not fair."
AQA chief executive Andrew Hall said: "I can certainly say I felt no pressure to do anything different to what we have always done," he said.
In an attempt to address concerns of "dumbing down" and ensure results were comparable, England's exams regulator, Ofqual, told exam boards they would have to justify any results notably different to those of previous years.
This year a number of new GCSE syllabuses, including English, mathematics and ICT, are being assessed for the first time. So extra measures have been taken to ensure grades are comparable.
The system known as "comparable outcomes" - which focuses on the proportion of students achieving each grade - sparked accusations that the exam boards were being asked to fix results.
In Northern Ireland, students bucked the national trend of falling GCSE grades and instead saw a slight improvement in their results.
A* to C grades went up by a small margin to 75.6%.