Figures released by the exam boards show that in Biology, Physics and Chemistry a higher percentage of those taking traditional exams gained A grades. Only in Maths was the proportion of A grades higher in the new courses.
In Chemistry and Physics, there was also a slightly higher percentage of students getting B grades.
However, figures for the four subjects show that the overall pass-rate is higher for modular courses, in which pupils sit a series of tests throughout their two-year course plus a final exam.
Earlier research from Newcastle University suggested that modular exams helped students to secure a grade higher than they would have done in a conventional exam.
Yesterday, exam boards were at pains to emphasise that there was no difference in standard between the two types of examination.
More than half the candidates took modular courses in Maths and Chemistry, about half in Biology and just under half in Physics.
Some English courses are also modular and these exams are due to be taken over the next two years in a growing number of subjects .
The proportion of A grades rose less than in previous years. It went up by 0.4 per cent to 16 per cent compared with 0.8 per cent last year and 0.9 per cent the year before.
Entries for Physics and Chemistry continued to decline, but those for Maths showed a rise.
Subjects with higher entries included General Studies, Business Studies, Psychology and Computing. In Economics and Classics the entry continued to fall.
Overall, the number of entries increased by a total of1.2 per cent.