Mike Cresswell told The TES the wholesale unitisation of the exams was probably not appropriate. "It will place an enormous burden on schools because of the sheer number of assessment opportunities this would create," he said.
His comments come after reports on Monday suggested the exam was about to follow A-levels and adopt a six-unit modular character.
This was based on a qualifications and curriculum consultation survey on the regulator's proposals to reform GCSEs for first teaching in 2009.
A question on the survey said unitisation turning GCSEs into modular qualifications could "enhance flexibility and choice", before asking respondents whether any problems could arise from this.
The next question said the QCA was proposing that at least half of all courses should be assessed at the end of two years of GCSE study and asked respondents if this was a good idea.
However, the QCA said this week it had no plans for all GCSEs to become modular. Science and some maths and modern languages exams already take this approach.
A spokeswoman said it would be up to individual exam boards to come up with courses, whether modular or more traditional, for accreditation.
Edexcel and OCR said it was too early to say whether they had any plans to bring out more modular GCSEs for first teaching in 2009.
Dr Cresswell said the AQA would listen to schools on the issue, but he advised caution. "The primary reason you have modular courses is to allow lots of curriculum flexibility. We are not convinced that is something which is needed or required at key stage 4," he said.
Pupils taking most GCSEs still need to follow the curriculum, he said, making different options less of a possibility than at A-level. And offering a modular system with much choice would pose organisational problems for schools.
But this does leave the door open for boards to gradually increase the number of modular exams on offer. The modular A-level has been cited as the cause of the increase in A grades of the exam.
Meanwhile, employers appear to be slightly more satisfied than they were a year ago with the English skills of school leavers.
Last summer, the Confederation of British Industry complained about low standards. A survey found 16 per cent of employers provided remedial literacy classes for recruits, while 14 per cent provided extra tuition for numeracy.
On Monday, the CBI revealed that a more recent survey of 507 businesses found the figure for literacy had dropped to 13 per cent, but 15 per cent said they were providing numeracy classes.
The CBI highlighted other figures showing 52 per cent of employers were dissatisfied with school leavers' literacy, and 50 per cent were unhappy with their basic numeracy. However, 92 per cent were happy with computing skills.
Kathleen Tattersall, chair of the Institute of Educational Assessors, said this was testimony to young people's abilities and the capacity of the GCSE to recognise modern skills.
The exam was condemned as "19th century" over the weekend. Professor Dylan Wiliam, deputy director of London University's Institute of Education, said it forced teachers to drill facts into pupils which would be of little use later in life. The exam had to be reformed to encourage pupils to think rather than prioritising knowledge regurgitation, he said.
But the Department for Children, Schools and Families said the exam was fit for the 21st century.
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