has learned, despite the fact that schools have no control over the exam timetable.
According to headteachers' leaders, because of the Department for Education's rule the league table scores of about 100 schools will fall, with up to 30 being "substantially" affected.
At Fullbrook School in Surrey, the proportion of pupils gaining five A*-C GCSEs including English and maths (5ACEM) this year would have been 69 per cent. But the DfE has said that the school's figure will actually be just 14 per cent - well below the "floor target" of 40 per cent.
GCSE English results for about 210 pupils - most of the school's cohort - have been excluded from the score because those students happened to have also sat a GCSE in English literature eight days earlier. Under the rules, if pupils take English literature first, their subsequent results from the combined English GCSE exam do not count towards league tables.
Anne Turner, headteacher of Fullbrook, said: "If the literature exam had by chance been timetabled after the English exam we would have been all right. Someone has clearly made up a rule without thinking through the implications.
"It is very disheartening for teachers who have worked flat out to get these amazingly good English results. It has just been so ridiculous. It is mismanagement by the DfE."
The school is one of scores of secondaries that have effectively been penalised for trying to improve pupils' chances by entering them for extra exams.
The Association of School and College Leaders has spent weeks trying unsuccessfully to persuade the DfE to change its position. Its general secretary, Brian Lightman, said: "Parents and the public can no longer have confidence in performance tables as they are incomplete.
"They do not give a true picture of how well students and schools have performed. Instead they show a skewed and unreliable picture based on the whims of political decisions."
Fullbrook's 2014 GCSE cohort were originally entered for a combined English GCSE, but the school later decided to also enter pupils for a full English literature qualification in order to broaden their knowledge of the subject.
Under DfE rules, because the pupils were timetabled to sit the English literature GCSE first they were deemed to have gone down a "pathway" that meant only a separate English language GCSE could then count in the league tables.
But the pupils had not been entered for English language, so their 5ACEM scores automatically became zero. The fact that they went on to get a good grade in the combined English GCSE was deemed irrelevant by the DfE as far as the league tables were concerned.
"The real irony is that the English language GCSE uses exactly the same exam paper as the English GCSE: the only difference is in the controlled assessment," Ms Turner said. "But we have now got a public figure against our name for a year of 14 per cent."
The problem stems partly from the government's rule, introduced partway through the last academic year, that only a pupil's first entry in a GCSE, rather than their "best entry", would count towards league tables.
The change was designed to stop schools attempting to "game" the league tables by tactically entering pupils for GCSEs multiple times. But because the rule is now being applied to distinguish between GCSE entries taken during the same summer exam season, it is also affecting schools that have entered pupils for English literature as an added bonus and, like Fullbrook, may never have used multiple entries.
"It is unreasonable that the order in which an exam timetable happens to fall can dictate a school's standing in the performance tables," Mr Lightman argued.
A DfE spokesperson said: "Schools were alerted to early entry changes in autumn 2013 and the English pathway rules in 2012. We do not intend to make retrospective changes to rules designed to ensure students take the right qualifications at the right time.
"To do so would be unfair to the majority of schools that acted in good faith on the rules that were in place at the time."