They say schools are confused about the advantages and disadvantages of "cashing-in", the term exam boards use when students opt to exchange their AS-level results for an official certificate.
Under the new A-level system, students who have done the first year of a course - completing three modules of study - can apply to the board for an AS certificate, showing the grade they achieved. Pupils who "cash in" their results in this way can enter the AS grade on their university application form; those who don't cash in, cannot.
However, if pupils do cash in and then decide they need to improve their AS score, they must retake all three modules, not just those in which they have done badly.
Pupils who take the AS certificate can still improve their final A-level score, by doing retakes of one or more first-year modules alongside their final A2 exams.
The situation in further maths is even more complex and the risks greater. Further maths students can choose which module results go toards their AS and A2, to maximise grades in both. But cashing in means the AS grade is based purely on the first year. Those who take a certificate could end up with lower grades than equally able peers who are free to combine results from first and second year in a more efficient way.
David Hart, general secretary of the National Association of Head Teachers, claimed the system was like Russian roulette. He said: "It is incredibly complicated and making the wrong choice could have serious consequences. It's typical of the complexities of the new post-16 curriculum."
Sue Kirkham, chair of the Secondary Heads Association education committee and head of Walton high school, Staffordshire, said: "There is total confusion out there and the official explanations are impenetrable."
A spokesman for the Joint Council for General Qualifications said: "For schools and colleges which have run modular A-levels in the past, much of this is familiar."
Education Secretary Estelle Morris confirmed this week that an inquiry into the A-level reforms would be carried out by the Qualifications and Curriculum Authority.