The number of entries to combined science fell by 27.6 per cent this year.
And the drop from 408,569 to 295,889 entries cannot be explained by a shift towards the chemistry, biology and physics GCSEs where entries remained broadly stable.
Many schools used to enter pupils for combined science - which is the most popular science GCSE - at the end of Year 10 and additional science at the end of Year 11.
But exams regulator Ofqual said this summer that many pupils who would normally have sat the exam at the age of 15 were waiting until next year to take the new 9 to 1 combined science or 9 to 1 separate sciences.
This year, there were only 960 entries for pupils aged 15 and under for GCSE science compared to 141,314 last year - a drop of 99.3 per cent.
And it is understood that this drop in entries has affected the overall results as more-able students who would normally have entered early are waiting until they are 16.
The figures released today show that the proportion of A* to C grades in GCSE science fell by 4.9 percentage points compared to last year.
Meanwhile, the proportion of A* to A grades dropped by 1.8 percentage points compared to 2016.
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