Michael Gove refused to intervene in the row over English GCSE grade boundaries on Monday as he warned the exams are "unfit for purpose".
Ministers should not "meddle" in decisions made by Ofqual, the independent exams regulator, the education secretary said.
He told MPs that it is down to Ofqual and exam boards to decide how to mark papers and rejected fresh calls to order a regrading of this summer's English GCSE.
He said that problems had arisen from the structure of the GCSE exam and that the government was reforming the system and removing modular exams.
For the first time this year, students taking GCSE English sat modular exams and submitted pieces of "controlled assessment" - coursework completed under strict classroom supervision.
Shadow education secretary Stephen Twigg said: "Over the past 10 days we've had countless examples of young people getting a D for work assessed this summer that would have got a C grade in January."
One head, Sally Coates of Burlington Danes Academy in west London, had said it is "blatantly unfair to move the goalposts without warning midway throughout the year", Mr Twigg said, asking Mr Gove if he agreed.
"I do agree that these examinations are unfit for purpose and need to change," the education secretary replied.
He later added: "Ofqual is an independent regulator accountable to Parliament. If ministers were to interfere in Ofqual's decisions, they would be meddling where they should not interfere."
Mr Gove said it was "opportunistic" for Mr Twigg to make the case for this.
He also suggested that there should be a greater degree of transparency about the grade-setting and marking processes.
"That is one of the reasons Ofqual exists as an independent regulator and it's one of the reasons why it should continue to do that job, not ministers," Mr Gove added.
The row over this summer's GCSE English results began as national GCSE results were published and it emerged that GCSE English grading boundaries had been altered between January and June.
Headteachers have predicted that thousands of pupils have been affected by the move, with concerns centring around those who were expected to get a C but ended up with a D grade.
On Friday, Ofqual announced it would be be inappropriate for either of the sets of exams to be regraded, as teaching unions continued to threaten legal action over the issue.
Pupils who are unhappy with their results have been told that they can resit the GCSE in November.
Hugh Bayley, Labour MP for York Central, asked Mr Gove if he would advise Ofqual to re-mark papers according to January's boundaries.
Mr Gove replied: "I share, sadly, the sadness that many teachers and many students will feel about what happened with GCSE English this year.
"I think it's appropriate that we all learn lessons about some of the mistakes that were made in introducing an examination modular in style, which was not best equipped to ensure that all students could perform well and be treated fairly."
But he added he would not tell Ofqual what to do.
"I will not because ... when he was supporting the government, Mr Ed Balls pointed out that Ofqual was an independent regulator of standards, independent of ministers reporting directly to Parliament. He said 'I am not going to second guess its work' and I fall to that position."
Earlier on Monday, Gove said students were let down by a "not entirely fair" exam system but attributed the blame to his predecessors.
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