She also says league tables should not "over-emphasise" certain grade boundaries in key subjects.
Your marks and the grade boundaries will be known to you and your school.
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And there was no evidence June's grade boundaries had been set "unduly harshly", its lawyers said.
It called for June's papers to be regraded in line with the January C-grade boundaries.
The regulator said the January papers were marked too leniently, but stood by the new June grade boundaries.
Exam boards stand accused of setting the grade boundaries too generously in January and too harshly in June.
These assessments appear to be at the heart of the change in grade boundaries in English GCSEs sat this year.
Mr Andrews said he acted after a report by his officials found the way grade boundaries were set was unfair.
It also suggested the grade boundaries had had to be moved in response to teachers "significantly" overmarking controlled assessment papers.
They did tell the WJEC to change the grade boundaries but it wasn't their idea - and they didn't want to.
Those concerns were around grade boundaries and not the exam board marking.
Exam boards panicked, and shunted grade boundaries to drag them back down.
Ofqual said grade boundaries did vary between units taken at different times.
It comes after grade boundaries were changed part way through the year.
For these reasons they say grade boundaries "would have to be set one or two marks lower than would otherwise be the case".
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Mr Andrews told MPs on Tuesday that his action was "appropriate" and intended to address an "unfairness" in the way grade boundaries were set.
Ofqual acknowledged grade boundaries had changed part way through the year, but stood by a new June grading system in a row over results.
The court heard claims that grade boundaries had been manipulated upwards in an attempt to avoid too many pupils being awarded higher GCSE grades.
They are threatening to seek a judicial review after thousands of pupils scored lower-than-expected results when grade boundaries were raised midway through the year.
Ofqual says that the June grade boundaries were set at the right level, but has acknowledged there was a problem with the January boundaries.
An alliance of heads and teachers' unions is continuing to press for June's papers to be regraded in line with the January C-grade boundaries.
Head teachers in England urged Ofqual to investigate when it was revealed that grade boundaries for the exams were changed part way through the year.
He said grade boundaries were set in a way that was unfair to candidates in Wales and they had been the victims of an "injustice".
BBC: WJEC says Leighton Andrews could damage Wales exam system
It would also mean that any unavoidable measurement error has a similar impact along the whole spectrum of marks, rather than being concentrated around grade boundaries.
The boards AQA and Edexcel have been defending their roles in shifting grade boundaries, on the second day of a judicial review at London's High Court.
The GCSE English controversy was about changes to grade boundaries, rather than marking - but English was also the subject that drew the most requests for re-marking.
Welsh Education Minister Leighton Andrews ordered the WJEC exam board to re-grade papers, saying the way that grade boundaries were set had been unfair to Welsh pupils.
Pupils from England, Wales and Northern Ireland were offered the chance to resit the papers free of charge after the row over the moving of grade boundaries.
Head teachers have claimed that English grade boundaries were manipulated downwards to ensure that the overall results did not increase - at the expense of individual pupils and their schools.
Most of the controlled assessment work was submitted in the summer and when examiners saw evidence of over-marking, exam boards raised grade boundaries, leading some pupils to receive poorer grades than expected.
BBC: GCSE English: Teachers' anger over generous marking claim
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