Only GCSE courses offered by sole Welsh exam board the WJEC will give full priority to the "distinctive approach" of the 14-19 learning pathways, it was claimed this week.
But Gareth Pierce, WJEC chief executive, also said any change of focus in the course content would be in line with those for England under a common standard.
His comments come one week after a new secondary curriculum was announced in England. Schools have been given the flexibility to teach English and maths to underperforming pupils and prune their timetables accordingly, with marking awarded for pupils' mastery of basic skills.
But it is unlikely the "back to basics" move in GCSEs will be seen in Wales until at least 2010. The immediate emphasis is on fulfilling the Wales-only requirement that every key stage 4 pupil spends one-fifth of their time on a vocational subject per fortnight by September 2008 as part of the 14-19 core.
An announcement on the future direction of the GCSE exam in relation to the Wales-only initiative is expected this autumn. But concern has already surfaced that continuing divisions between the Welsh and English curricula could lead to a lack of choice and increased separation in study programmes something the WJEC hotly denies.
Dr Phil Dixon, of the Association of Teachers and Lecturers Cymru, said: "Will we see a situation where students who take GCSE courses with English-based exam boards will not have the same policy-driven direction as that offered by the WJEC? Will it mean that schools feel they have to opt for the WJEC instead of an English alternative?
"It has always been the case that schools opt for the courses that are guaranteed to give better pass rates."
The Assembly government says that new courses in some subjects will take place from September 2009. But moves towards "improved coverage of the basics" in maths and English will probably not be announced until 2010 after the results of WJEC pilot courses.
A spokesperson for the Assembly government said changes to the curriculum for Wales in September 2008 will focus more on key skills and flexibility.
"Proposals this year presented a curriculum for Wales that is skills-focused and learner-centred. It will give schools greater flexibility in teaching. England is piloting GCSEs in English, maths and ICT but on a different basis. The exam system in Wales, England and Northern Ireland recognises differences but retains common standards."