Most schools are following revised science courses
Half of England's comprehensives did not offer physics, chemistry and biology GCSEs last year, figures show.
The figures - requested by the Tories - show that in two areas not a single pupil studied the separate sciences.
The government has said that every pupil doing adequately in science by the age of 14 should be able to pursue the three subjects.
In the new curriculum, most schools do a core science GCSE with "additional science" for those who are interested.
These have supplanted the double science course that most pupils followed from the early 1990s.
Separate or "triple" science GCSEs in physics, chemistry and biological sciences are the norm in grammar schools and independent schools.
The figures show that, on average, 46% of comprehensives entered at least one pupil for separate sciences.
GCSE ENTRIES 2005 / 2008
Physics: 30,954 / 52,894
Chemistry: 31,248 / 53,309
Biological sciences: 32,838 / 58,855
DCSF achievement and attainment tables, maintained schools
But no pupils at all in two local authority areas - Islington and Slough - were entered for separate sciences last year, although Islington says two of its eight schools do now offer them.
Just under a quarter of exam entrants (23.4%) did only core science in comprehensive schools, while 57.2% took core plus additional science.
Shadow schools minister Nick Gibb said: "It is truly shocking that there are whole areas of England where not a single child has the opportunity to sit separate science GCSEs.
"Without a good understanding of physics, chemistry or biology at the age of 16, it is almost impossible for pupils to get top marks in these subjects at A-level and progress to a science degree at a top university."
Schools Minister Sarah McCarthy-Fry said: "The number of pupils taking triple science has increased significantly since 2007 and we are investing £6m over the next three years to double this number."
But she added: "It is misleading to suggest that pupils who don't take triple science are not receiving a strong grounding in physics, chemistry and biology.
"Through core and additional science, pupils will receive a good foundation in all three sciences which will set them up for further study at A-level."
The Association of School and College leaders said the figures were misleading because they related to students who began their GCSEs in 2006.
"The entitlement to triple sciences took effect in 2008 so students starting triple sciences under the entitlement will not appear in the GCSE results until 2010," said policy director Malcolm Trobe.
"Other schools may be offering three separate sciences but no student is choosing to take all three."
The pupil entitlement to be taught triple science is not however matched by an obligation on schools to teach the three subjects.
Dilemma over science entitlement