Science and maths could become "two-tier" subjects at GCSE, with only a minority of pupils taking exams that are regarded as a proper foundation for A-level, subject specialists have warned.
They believe that government attempts to boost interest in the subjects may backfire, with even fewer pupils opting to study them in the sixth form.
Their fears follow last month's announcement by the Treasury that every pupil who achieves level 6 or above in key stage 3 science will be entitled to study three separate sciences at GCSE from 2008.
The Royal Society has questioned how the proposal, announced in an update of the Government's 10-year science strategy to coincide with the Budget, can be made to work.
Professor Martin Taylor, its vice-president, welcomed the Chancellor's emphasis on science, but said he understood that schools would not be forced to offer pupils physics, chemistry and biology.
It was therefore not clear how pupils could be guaranteed the chance to study them, especially as many schools struggle to recruit physics and chemistry specialists who could teach the subjects.
Most students take double science GCSE, rather than single sciences. New courses will be introduced from September which will see many pupils opting for a core course in general science followed by either an academic or a vocational option.
But the Treasury appears to be backing single sciences as the best preparation for A-level. A document it published to co-incide with last month's announcement said that state pupils taking single-science GCSEs were more likely to get an A or B grade at A-level than those taking double science.
The Royal Society is concerned that the Treasury's move could result in only the triple science option being seen as a proper foundation for A-level.
It fears that with few pupils given access to triple science, the number taking A-levels in physics and chemistry - which has slumped recently - could fall still further.
Professor Taylor said: "We hope this new entitlement does nothing to suggest, or indeed create, a two-tier system in which only those doing three GCSEs are considered properly equipped for progression to A-level."
The concerns are echoed in maths. Ruth Kelly, the Education Secretary, announced in March plans for a new further maths GCSE designed to stretch more able pupils. Some teachers fear the exam, to be introduced within four years, will be offered only to a minority of pupils.
A Department for Education and Skills spokeswoman said: "We will encourage schools to make triple science available to all pupils who could benefit.
Double science, and its equivalent under the new GCSEs, remains a good preparation for A-level."