The finding, in the most extensive research of individual school results, raises questions about the extent to which inner-city schools are abandoning academic study to boost their league table places.
It shows that pupils taking a vocational qualification, worth four GCSEs, spend the same amount of time in class as that devoted to a single maths GCSE.
The TES analysis suggests the tables, in which popular vocational courses count as four GCSEs, may be encouraging schools to avoid more academic provision.
John Dunford, general secretary of the Association of School and College Leaders, said: "This shows very clearly how league tables have skewed the curriculum."
Our study shows that, at five of the seven most improved schools in England last year, no pupils passed double science GCSE at C or better. At nine of the 104 schools no pupils got even a C in history, while the same was true in some schools for geography and languages.
At the North school, a secondary modern in Kent named as one of England's two most improved schools, no pupils got a C or better in double GCSE science.
No pupils took GCSE science at the other first-placed school, Sir John Cass, in Tower Hamlets, east London. All took general national vocational qualifications, which many believe are not suitable for progression to A-level.
Waverley comprehensive, in Birmingham, the third most improved school, failed to enter any of its 112 pupils for science GCSE, and only entered five pupils for European languages. Nine pupils passed geography, and three history.
Professor Alan Smithers, of Buckingham university, said GNVQs, popular with schools due to league-table pressures, were not valued by employers and therefore of little use to their pupils: "How is a pupil who wants to be a doctor or a physicist, to pursue that career if they are not offered the chance to study academic science at school?"
However, several schools said GNVQs motivated students and made them feel more positive about all subjects they studied.
Of the top seven listed schools, the average figure for pupils achieving a C or better in double science GCSE was 8 per cent; in at least one European language, 9 per cent; in history, 6 per cent; and in geography, 5 per cent.
Ministers want all pupils to have a choice of vocational or academic courses. But the numbers avoiding academic subjects suggest these are options for a small minority in some comprehensives.
The Government says that GNVQs should be worth four GCSEs as schools devote more time to teaching them. But our analysis shows the top 30 most-improved schools spent 3.7 hours a week on GNVQ ICT, compared to 3.5 hours for maths GCSE.
The TES compiled the data with Roger Titcombe, a retired head, and statistician Roger Davies.
NEWS 6, leader 22
Additional research by Stephen Manning