Ministers are planning scrap International GCSEs from school league tables as part of the government’s major overhaul of the exam system.
The move, expected to be introduced in 2017, will mean thousands of schools that currently offer the qualification will be affected and could plunge down league tables.
It is understood that under the proposals, only reformed GCSEs in maths and English could count in performance rankings in the future.
New reformed GCSEs in maths and English, which feature little to no coursework and exams at the end of the course, are to be introduced into England's schools in September next year, with the first exams taken in the summer of 2017.
Under the latest plans it is understood that only these exams will count in league tables from 2017, a move that effectively means that IGCSEs will not be accepted qualifications.
Currently, both IGCSEs, which have long been favoured by many private schools, and GCSEs count towards annual league tables.
It is thought that the decision has been taken as IGCSEs generally do not share the same construction as the government's reformed exams in areas such as end-of-course exams and coursework.
The move leaves the door open for IGCSEs to be reintroduced to league tables at a later date, if changes are made to ensure they are of a similar design to new GCSEs.
New GCSEs in other subjects such as science, history and geography are due to be introduced in 2016, with the first exams taken in 2018. It is understood that IGCSEs in these subjects are set to be dropped from performance tables at this point.
Brian Lightman, general secretary of the Association of School and College Leaders, criticised the move saying the decision has come “far too late” and will have serious impacts on thousands of pupils.
"Schools were encouraged to believe that IGCSEs would continue to be accepted and have planned accordingly," Mr Lightman said. "It is very late in the day for these changes to be introduced and this is causing difficulties for those schools which, in all good faith, had planned to continue using IGCSE qualifications.
He added: "It also has serious consequences for young people. Parents and young people are finding it difficult to make sense of these piecemeal changes."
Back in 2012, education secretary Michael Gove suggested schools consider switching to the IGCSE as it would provide “appropriate preparation” for the new-look GCSEs.
In recent years there has been a surge in IGCSE entries, particularly in English, which came amid major changes to GCSEs in the subject.
Many schools, particularly those in the private sector, argue that IGCSEs are tougher than current GCSEs.
But last year, headteachers also suggested that some schools were entering pupils for IGCSEs because they believed the tests were "easier".