Ministers plan to introduce new "world-class tests" for the brightest students to counter claims that the A-level "gold standard" has been diluted.
But the tests may only be available in the six most popular A-level subjects: English, maths, physics, chemistry, history and French - under plans being considered by the Qualifications and Curriculum Authority.
But heads argue that the proposals would be "totally unfair" preventing many able students from taking tests in their best subjects.
The tests were unveiled in March to run alongside new-look A-levels to be introduced in September 2000. They will replace the increasingly unpopular S-level papers which were taken by fewer than 5,000 pupils last year.
John Dunford, general secretary of the Secondary Heads Association, said: "It makes the prospect of universities setting their own tests more likely. At the very least, the tests must be available in the 12 most popular A-level subjects."