Nearly one-third of all specialist science schools are unable to muster even one GCSE physics candidate, The TES can reveal.
The figures, obtained by the Conservatives through a parliamentary question, led them to call on the Government to "get a grip" on the issue.
The statistics also suggest an uncertain future for specialist schools in general, with both Conservatives and Liberal Democrats claiming they fail to deliver on their promises.
A parliamentary question, submitted by shadow schools minister Nick Gibb, revealed that in 2008 122 out of 433 schools did not enter a single pupil for physics GCSE.
Last week, the Conservatives revealed that pupils eligible for free school meals were 25 times less likely than their wealthier peers to take separate sciences. The Tories also claim that barely 2 per cent of pupils eligible for free meals sit GCSE physics or chemistry.
And it emerged earlier this month that in 2008 neither Islington in north London nor Slough in Berkshire had a single child in any comprehensive school sitting separate sciences at GCSE.
"Science teaching is in real trouble," Mr Gibb said. "Nationally, two- thirds of pupils don't take GCSEs in the separate sciences. And in some areas not a single comprehensively educated pupil takes these key qualifications. Now we find out that the problem even extends to schools with a science specialism.
"We urgently need to get a grip on this so that all pupils have the chance to take GCSEs in physics, chemistry and biology.
"That's the best way to prepare for study at top universities, and to ensure our country has the knowledge it needs to compete in the global economy."
The Lib Dems urged the Government to scrap the specialist schools programme, saying the money could be better spent on teacher recruitment.
David Laws, Lib Dem education spokesman, said: "The specialist schools programme is clearly not working very well. Ministers need to scrap this central programme, fund all schools at the specialist level, then focus on recruiting more excellent science teachers into all our schools."
Charles Tracy, head of pre-19 education at the Institute of Physics, said: "The largest problem with physics is that it is often taught by teachers with a specialism in a different subject. Studies have indicated that pupil participation and success in a subject are linked to the confidence and ability of its teachers. We strongly advocate every school having at least one specialist physics teacher. Specialist science schools ought to be trail blazers in this regard."
A spokeswoman for the Department for Children, Schools and Families said three-quarters of specialist science colleges offer the three separate science GCSEs.
She said: "An independent report said physics take-up improved from 43 per cent to 70 per cent in specialist science colleges between 2003 and 2007. However, like most schools they will enter some of their students for core and additional science rather than the three individual sciences, depending on what best suits the individual pupil."