A fifth of state school sixth forms entered no pupils for A-level physics last year, while one in 10 had no maths entrants.
The government statistics, released this week, have exacerbated fears of a growing educational divide between schools.
Headteachers' leaders say the figures indicate that pupils are deserting traditional subjects because they view them as too difficult.
The figures show that in 2007, 19 per cent of state sixth forms in England had no A-level physics entrants, while 15.6 per cent entered no one for chemistry, 13.2 per cent entered no one for biology, 10.6 per cent entered no one for maths and 16.6 per cent did not enter anyone for more than one science A-level.
David Laws, Liberal Democrat schools spokesman, said: "There is a risk that some of these subjects will become the preserve of the top performing state and private schools, which I don't think is acceptable.
But Hitchin Boys' School in Hertfordshire has been bucking the trend. Last year 41 Year 12 boys were studying A-level physics, compared to 28 in 2006 and 13 in 2005.
Keith Wadsworth, the head, said science had been effectively in crisis at the school about five years ago but refurbished facilities and a staff recruitment drive had turned things around. "We made a decision that science had to be a priority," he said.
Earlier this month, government figures revealed that fewer than one in three state school pupils had the option of taking separate physics, chemistry and biology GCSEs, compared with more than two-thirds of private school pupils.
Sue Johnston-Wilder, chair of the Association of Teachers of Mathematics, said pressure on teachers to deliver better results was not helping to make maths interesting and could be causing pupils to drop it.
Last month, ministers announced a pound;34 million three-year package to help boost technology, engineering, science and post-16 maths figures.
Derek Bell, chief executive of the Association for Science Education, said the money would help, but expressed concern that 14-19 diplomas might further affect A-level take-up.
But Clare Thomson, of the Institute of Physics, said that arrangements allowing students to study at neighbouring colleges meant that take-up was not as bad as it seemed.
Martin Ward, deputy general secretary of the Association of School and College Leaders, said schools dropping A-levels for the International Baccalaureate also had affected the figures. But he added: "Students are seeing subjects such as maths, physics and modern languages as more difficult than others and shying away from them."
The Department for Children, Schools and Families said changes to the science curriculum, designed to make it more engaging, fun and relevant, were on the right track.
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