Crucial GCSE scores at more than 1,700 schools and colleges could fall this year after the government decided that the IGCSEs used by the institutions will not count fully in the league tables.
Headteachers have spoken of their anger at finding out about the ruling in the autumn after pupils had already taken the exams. The decision will push some schools below the government's minimum benchmark of 40 per cent of students gaining five A*-C GCSEs including English and maths (5ACEM).
The Department for Education has ruled that IGCSEs from the AQA and WJEC exam boards taken this summer will not be treated as GCSEs in performance tables, even though more established IGCSEs offered by two other exam boards will be.
Officials have admitted that the decision does not have anything to do with the quality or content of the qualifications - it is purely "a matter of timing" in terms of when the IGCSEs were introduced.
Schools entered pupils for the exams on the understanding that they would count fully towards the 5ACEM threshold. Neil Walker, headteacher of Benfield School in Newcastle, which has been pushed below the floor standard, said he felt "devastated" by the decision.
Instead of being recognised as full GCSEs, the IGCSEs will come under the bracket of the two non-GCSE qualifications that schools can put towards the 5ACEM benchmark.
WJEC said it was told by the DfE last year that its IGCSEs would count fully in the league tables.
When informed of the situation by TES, a spokesperson for AQA, England's biggest school exam board, said: "This news came as a complete surprise to us. We are assuming it is just a mistake that the department will now put right." After learning that the DfE was standing by its decision, she said AQA appreciated that "some schools and colleges will be disappointed".
Anne Davis, principal of Matisse College at Longfield Academy in Kent, said: "If you have a product you are selling, you should know absolutely everything about that product and that includes whether it counts, doesn't count, double counts, whatever.
"We can't see a rationale for this. And why tell us so late in the day? I don't think anyone at the DfE is thinking this through."
Many secondary schools have already been frustrated by a retrospective move, announced part-way through the last academic year, to clampdown on multiple entries to GCSEs by allowing only first entries to count towards league tables.
The IGCSE decision is out of line with previous government policy, which has been to encourage schools to use the qualifications as an alternative to domestic GCSEs.
In May 2013, AQA announced that its English and maths IGCSEs had received the DfE's "official seal of approval" and would be "fully included in school league tables".
In England this summer, 1,636 schools and colleges entered students for AQA IGCSEs and at least 86 entered students for WJEC's versions.
Duncan Baldwin, deputy policy director at the Association of School and College Leaders, said: "We believe it is unfair to change how qualifications contribute to performance tables when courses have already started in schools. Changing the rules halfway and constantly meddling is deeply unhelpful and undermines schools' confidence in performance tables."
Documents published by the DfE suggest that the decision may have been taken in the summer. By September it was clear that there would be a distinction in performance measures between IGCSEs offered by Cambridge International Examinations and Edexcel and those introduced subsequently by AQA and WJEC.
The move is separate from the government's decision to start removing IGCSEs from school league tables from 2017, when completely new domestic GCSEs with a numerical grading system will be phased in.
AQA said it was "confident" that the DfE would include its IGCSEs in performance measures for the 2015 and 2016 results. TES understands that the exam board is not being asked by the government to make any changes to the qualifications.
Hugh Lester, from WJEC's qualifications directorate, said: "We are discussing this issue with DfE, as confirmation received in May 2013 stated that this qualification would contribute fully in the 2014 school performance measures."
The DfE said it was keeping its rules on IGCSEs "under review". A spokesman said that AQA and WJEC qualifications could count towards the 5ACEM and English Baccalaureate league table measures this year "as one of [schools'] two non-GCSE qualifications".
`It is quite simply not good enough'
The decision to treat AQA IGCSEs as "non-GCSEs" will have severe repercussions for Benfield School in Newcastle.
The comprehensive entered 47 pupils for the English language version of the qualification believing it would count as a GCSE. But the IGCSE's lower status means the proportion of students gaining five A*-Cs including English and maths has fallen from 42.5 to 39.6 per cent, pushing the school below the floor standard.
"We are due an Ofsted inspection this academic year, and the way the regime is, this will make it very difficult for us to get anything better than `requires improvement'," says Benfield headteacher Neil Walker. "Had it been made quite clear, we would never have opted for that qualification in the first place.
"It states on the AQA website that the IGCSE is an accredited qualification, and for the Department for Education to discount it for no rational reason makes you feel let down.
"The fact that the department could change it but won't and says it is a timing issue - that is quite simply not good enough. We have tried to talk to AQA and the department about this and there seems to be a distinct lack of willingness to do anything or realise the impact that it can have on schools."