The Advisory Committee on Mathematics Education said some pupils will find their options closed at 13 if ministers press ahead with plans to introduce the second exam. Numbers taking the subject at A-level could also plummet, it said.
The Government wants to offer the second GCSE to reflect the amount of time pupils spend on the subject and its central place in the curriculum.
However, there is controversy about how it would do so.
The second GCSE will address more conceptual and theoretical aspects. But ministers are not stipulating that all pupils must study it if they want to move on to A-level maths. Instead, they take the line that pupils should be able to take the A-level on the basis of a single maths GCSE which, from 2010, will include compulsory functional skills tests, that cover only the subject's basics.
The danger will be that some schools, seeing the second GCSE as voluntary, will not offer it to any of their pupils, leaving them with only a dumbed-down version of the current exam.
One of the committee members, Professor Margaret Brown, of King's College, London, said: "The danger is that the 'compulsory GCSE', without the second GCSE, will not provide the proper foundation for further study at A-level.
"Pupils must not be misled on this issue. Without taking the two GCSEs they would have to undertake some form of supplementary study to face the demands of A-level."
The committee's intervention is highly unusual. Set up five years ago to mediate between maths subject associations and the Government, it has usually avoided public controversy. It wants ministers to say that at least 60 per cent of pupils should take the second GCSE.