Ministers want to avoid a repeat of the problems over languages. When it was decided to make that subject optional at key stage 4 from 2004 numbers plummeted.
Ministers fear curriculum changes, designed to encourage more pupils to take science A-level, could lead to less academic pupils abandoning all but the most basic elements.
Jacqui Smith, schools minister, has told headteachers she wants the numbers studying two science GCSEs to remain at around the current 80 per cent of pupils.
"The Government, public and business leaders need to be assured that all schools will enable pupils to access appropriate qualifications at 16 and beyond," she says in a letter to secondaries. "It is vital that students understand that only particular combinations of subjects will provide the basis for advanced level study in science."
From September, all students beginning science will study a slimmed-down core curriculum, leading to a single GCSE. Most are then expected to opt for a second exam in the subject, in options ranging from vocational science and a generic academic course to individual science subjects.
Sue Kirkham, president of the Association of School and College Leaders and a member of the Qualifications and Curriculum Authority board, feared schools might just offer the basic course.
Concerns would be greatest at secondaries where staff shortages made it difficult to find teachers for specialist subjects, she said. And some pupils, fearful that the sciences were harder than many other GCSEs, could vote with their feet.
Ms Smith said innovations including the introduction of teaching and learning reviews and school self-evaluation created "short-term"
difficulties last term.
The letter said: "I know from my visits to schools and other conversations with school leaders that last term not only felt long but was also hugely challenging for heads, school staff and governors."