England's schools face "disruption" after ministers changed their minds about which GCSEs will count in school league tables, says the heads' union ASCL.
Ministers are phasing in new, toughened GCSEs and originally said the old ones would count in league tables during the transition to the new exams.
Now old GCSEs will count for students but not for school accountability.
The government said the move meant consistency between exams.
Ministers have pushed through a range of changes to GCSE and A-level exams which require complete new syllabuses and examinations to be drawn up, approved and accredited.
English and maths GCSEs are being introduced this year, with other subjects to reach schools for teaching in 2016.
Many schools, however, run three-year GCSE programmes, which start in Year 9, with some exams being taken in Year 10 and some in Year 11.
This enables students to spread exams over two years, rather than having to take a large number of exams in one, and creates space in the timetable to focus on key subjects such as English and maths in Year 11.
Students starting these three-year courses in September cannot take the reformed GCSEs in Year 10 because they are not yet available. So, schools had planned that GCSEs taken in Year 10 would be in the unreformed older courses.
ASCL president Peter Kent said: "School leaders are now left with an invidious dilemma.
"They must either change decisions already made with students and parents, and rip up existing timetables, to make sure everybody takes the new reformed GCSEs, or press on with the plans they already had in place and accept that their performance tables will suffer because they will include unreformed GCSEs.
"This has plunged schools, students and parents into disruption and uncertainty."
Dr Kent said: "It is absolute nonsense. These are perfectly valid qualifications which reflect the achievements of students, but which schools will not be allowed to include in their figures.
"One subject which is particularly affected is religious education because this is a GCSE which is sat in many schools in Year 10."
Mr Kent, who is also head teacher of Lawrence Sheriff School in Rugby, said: "In my school we have decided to take the hit on performance tables, but there is no right answer. It is a case of damned-if-you-do and damned-if-you-don't.
"ASCL is very disappointed that despite clearly showing to ministers and officials that this decision is profoundly unfair, they have refused to budge. We have asked them to be reasonable, but our appeal has fallen on deaf ears."
A Department for Education spokesman said: "Our new world-class GCSEs are raising the bar so more young people have access to the world-class education they deserve, equipping them with the skills they need to get on and succeed in life.
"We want pupils to be taught these new gold standard GCSE courses as soon as possible. "