Ministers will not fund IGCSEs in English, maths and science for under-16 state school pupils because they could lead to them missing "vital" parts of the curriculum such as Shakespeare.
A re-branding of the O-level-style exams as Cambridge International Certificates (CIC) - to prevent confusion with conventional GCSEs - had led to government funding for them in nine other subjects.
But Iain Wright, schools minister, this week ruled out doing the same for certificates in statutory curriculum subjects. "Approval of CICs would present a risk to the focus on the vital curriculum elements," he said. "For instance, young people would be able to opt out of answering questions on Shakespeare."
The Government said the physics, chemistry and biology certificates did not explicitly cover elements of the curriculum on data, evidence, theories and explanations, practical and communication skills and the applications and implications of science.
It said the maths certificate omitted requirements on applications and problem solving.
Kevin Stannard, from Cambridge International Education - the board offering the certificates - said he was "surprised and disappointed" that state pupils were being denied access to qualifications available in other sectors and 150 countries.
But John Dunford, general secretary of the Association of School and College Leaders, said: "We do not want a market in qualifications. Exams are not items on a supermarket shelf."
The move will be less well received in the independent sector, where more than 90 per cent of top schools offer at least one of the certificates.
The lack of equivalent state school funding scuppers any chance of the certificates in the core subjects being included in school league tables, although the other nine subjects will be from next year. But the Tories said they would approve all certificates.
The Government has validated all the certificates for state school funding for 16- to 19-year-olds.