Education Secretary Michael Gove has refused to intervene in the row of GCSE English grades, despite admitting pupils have been treated unfairly.
He told MPs it was up to England's exams regulator Ofqual to uphold standards and oversee marking and grades.
Schools have threatened legal action after grade boundaries were moved dramatically part way through the year.
Labour's Stephen Twigg said it was "rough justice".
Mr Gove had been called to explain to MPs exactly what happened in this year's exams sat by pupils in England, Wales and Northern Ireland.
But he told the Commons it was not his place to get involved with decisions about marking and exam grades.
In response to a question from shadow education secretary Mr Twigg, he said: "If ministers were to interfere in Ofqual's decisions they would be meddling where they should not interfere."
It was the examinations themselves that were at fault and needed to change, he stressed.
But Mr Twigg said it was "rough justice" that young people were getting a D grade in the summer that would have got a C grade if it had been submitted in January.
Labour MP Philip Wilson said if the athlete Mo Farah had won the 10,000m final at the Olympics but was then told he had to run a further 10,000m before he could claim his gold medal, "we would say it was wrong."
"So why is it right to change the way GCSE exam results are marked halfway through the academic year which is what has happened this year?"
Earlier the education secretary told BBC Radio 4's Today programme: "My heart goes out to those students who sat the exam this year because I don't think the exam was designed in the most appropriate way.
"Everyone who sat the exam was treated in a way that either wasn't fair or appropriate."
But politicians could not act as "chief examiner", he added.
He said the structure of the exam itself had been "unfair and inappropriate" and he was planning to reform GCSEs in England as soon as possible.
The exam in question was modular in nature, with pupils sitting chunks of the syllabus, throughout the year.
It also featured new controlled assessments, overseen by teachers in class, which were introduced to address concerns about GCSE coursework. These assessments appear to be at the heart of the change in grade boundaries in English GCSEs sat this year.
Mr Gove has already set in place reforms to England's GCSE that prevent repeated retakes of parts of the qualifications. Pupils will begin these new courses this autumn and sit exams in 2014.
And he has said he intends to return to what he describes as a more rigorous an O-level style qualification, promising more details later in the autumn.
However, under his reforms the majority of pupils would sit a single examination rather than being split into those taking lower valued CSEs and more academic O-levels.
"What we need to do is have an examination which has all the rigour of the old O-level but it's sat by the majority of students," he added.
He added the new qualification would be so rigorous "nobody could imagine there has been any grade inflation or deflation".
But general secretary of the National Union of Teachers Christine Blower said Mr Gove had to accept the situation was "utterly unfair and unacceptable".
"Now is not the time to stand on the sidelines debating the value or otherwise of GCSEs.
"There needs to be an independent inquiry into how pupils who would have achieved a C grade in January, got a D in June.
"There also needs to be an immediate regrading not re-marking of this year's English exams."
She added that if Mr Gove did not intervene, legal action could be the only course of redress left open to schools.