Splitting all A-levels into six "modular" chunks will damage arts subjects, inspectors have warned the Government.
Only a few subjects, such as maths and physics, are well-suited to a modular approach which tests candidates throughout the course.
Others, including English and modern languages, may lose depth because students are tested before they can develop a "mature understanding", according to a new HM Inspectorate report on modular exams taken between 1996 and 1998.
Modular courses could restrict the brightest pupils, say the inspectors, who want exam certificates to show whether students sat a linear or modular course.
Although they concluded there was no evidence that one style of course was easier than the other, they did say that sixth-formers who take modular exams may not gain such a good overview of their subject as classmates following a traditional course.
From September 2000, all A-levels will have a modular structure. They will be split into two sections of three modules each with the first year consisting of a stand-alone "advanced supplementary" exam. Students will be encouraged to take four or five AS-levels before choosing three subjects to continue to full A-level.
Modular exams do not always stretch the brightest students, but can boost the performance of the least able, said inspectors. The courses had expanded so rapidly that exam boards had not been able to develop reliable mark schemes or train their examiners properly, they added.
Ministers are already trying to safeguard the A-level "gold standard" by limiting the number of times students can re-sit modules and insisting on a final "synoptic" module which requires them to demonstrate their overall subject knowledge.
But inspectors said some synoptic modules were poorly designed and that assessment needed to be tightened up.
Sixth-formers taking modular exams could have different teachers for each module which fragmented the course and prevented many candidates making mental links across the syllabus.
David West, head of the Office for Standards in Education's post-16 division, said: "Sometimes links between modules are lost because they are taught by different teachers. The modular approach can also constrain teachers in the way they teach the subject."
Three years ago only one-fifth of A-level entries were modular, mainly in maths and the sciences. Last year more than half of entries were modular.
The Government has insisted that schools can still opt for linear courses by making candidates take all six modular exams at the end of the course.
But inspectors warned this would be unpopular with schools and, said Mr West, linear A-levels would "wither on the vine" unless stronger action was taken.
Headteachers' leader David Hart said he was "extremely concerned" at the suggestion that exam certificates distinguish between linear and modular A-levels. He said: "This would divide students into sheep and goats and would devalue the achievement of a number of students."
The report, Modular GCE AS and A-level examinations 1996-1998, is published by The Stationery Office, pound;6.95. Telephone 0171 873 9090