Michael Gove insisted that the worst GCSE grades for over 20 years were not the result of political pressure as a row erupted between the Education Secretary and schools over concerns that the exams had been marked too harshly.
He told BBC News that any changes in grades were the result of "independent judgments made by exam boards".
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 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.
However Brian Lightman, general secretary of the Association of School and College Leaders, called for an investigation into the matter and accused the government of yearly "tinkering".
He said: "The big issue, schools are telling us, is at the C/D borderline in English.
"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."
Thursday'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. The exams were first taught in 1986, with the first exams taken in 1988.
The results also show that the proportion of entries awarded at least a C in the key subjects of English, maths and science have fallen.
The national figures show 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.