Science Year head Mike Tomlinson has questioned the benefit of pupils studying double science GCSE rather than separate physics, chemistry and biology.
Double science, which is worth two GCSEs, was introduced to encourage pupils to continue with sciences to 16. It has proved popular with just over 1 million entries this year. By contrast 46,500 took physics, 47,000 chemistry and 49,000 biology.
However, there is concern that double science is failing to prepare pupils for further study, with some teenagers struggling to jump from GCSE to A-level. The number of pupils going on to complete a full A-level in biology and chemistry fell this summer, although the numbers taking physics rose.
Mr Tomlinson, former chief inspector of schools, said double science had been successful but it was time to reassess it. He said a number of schools had abandoned it to revert to lessons in chemistry, biology and physics.
A government-backed report by Sir Gareth Roberts, president of the Science Council, pinpointed transition from GCSE to A-level as a major problem.
This is likely to be exacerbated by the growth in vocational alternatives to science GCSEs. At Sir John Cass Foundation and Redcoat school, in Tower Hamlets, east London, all pupils were entered for intermediate GNVQ in science, worth four GCSEs.
The percentage of pupils gaining five top grades rose from 36 to 71 per cent - the first school in the inner-city borough to get above 60 per cent good GCSE passes.
The science GNVQ national pass rate was 74 per cent this year, compared to 53 per cent in double science GCSE. Entry numbers nearly doubled to 1,887.
Vocational GCSEs in the subject are being taught from this term for the first time and the Qualifications and Curriculum Authority is about to pilot hybrid science GCSEs, which allow pupils to study a common core and then branch off to vocational or academic modules.
Sir Gareth's report warned that while reforming the GCSE could make science more popular, it could create a more varied intake to A-level courses, making a smooth transition even more difficult.
Mr Tomlinson, speaking at the British Association Festival of Science, in Leicester, was launching the pound;4 million iniative, Planet Science, the successor to the Government's Science Year. It aims to narrow the attainment gap in science between different ethnic groups and is conducting research into the issue.
It will encourage schools to take part in extra-curricular science activities. "It may be nothing more than the fact that they cannot afford the bus. We can help with that," said Mr Tomlinson.
Supermarkets are to distribute leaflets telling parents how to help their children with science homework. Booklets, aimed at the parents of nine to11-year-olds, will tackle common homework subjects. It will also reveal, for example acids and alkalis that can be found in the kitchen.
Mr Tomlinson said: "Children turn to their parents for help with science homework, but many parents feel very lacking in confidence in giving that help."
Reacting to criticism that Science Year had not involved teachers enough, he said the intention was to do better.