Teacher training schools will have to tell the Government whether their general science PGCE students specialise in physics, chemistry or biology, as part of a drive to address the shortage of science teachers.
Last year, more than a thousand graduates signed up for combined or general science PGCEs, compared to 821 for biology, 465 for chemistry, and 311 for physics.
The move has been welcomed by the Royal Society and other science bodies, as it will help the Government see the true depth of specialist science teacher shortages.
It is feared many of the general science graduates are biologists, which are not in as short supply as those for physics and chemistry.
A report by the society late last year called for more research to be carried out into why universities offered the combined science PGCE, and why trainees opted for it over specialist courses.
It also called for England's General Teaching Council to keep more up-to-date detailed records of teachers' degree subjects and teaching specialisms.
Hilary Leevers, assistant director of the Campaign for Science and Engineering, said: "It is a good idea to get the intake to define itself in terms of subject specialism, so we know where the students on combined courses are coming from."
Information on the make-up of the workforce is becoming increasingly essential, because from next year all science specialist schools will have to offer separate sciences at GCSE as an entitlement.
All pupils with level 6 or above at key stage 3 will also be entitled to study separate subjects.
Research from Buckingham University last year suggested that pupils who study separate sciences at GCSE are more likely to take them to advanced and degree level.
The rules on reporting the specialist make-up of combined science courses in census returns will start in September, and will only apply to PGCE courses aimed at teachers of GCSE and A-level.
A document from the Training and Development Agency for Schools said: "This change does not prevent providers from offering broad-based science training at key stage 4 but, in accordance with the guidance to the standards for the award of qualified teacher status, providers will be expected to identify a principal science."
The agency said that it had to know the numbers of physics and chemistry graduates recruited to all science courses so it could distribute the pound;1,000 in extra funding each trainee carries.