The Department for Education and Skills has told the Specialist Schools Trust it is unlikely to agree bids from the 700 schools where fewer than a quarter of pupils get at least five A*-C grade GCSEs, unless results are rising rapidly.
Some struggling schools, including Parkside technology college in Plymouth, got specialist status in the past in an attempt to jump-start improvements.
Janet Waters, head of curriculum support for the trust, said the department felt such schools should focus on raising their results rather than making bids.
But the National Union of Teachers said the move was a "double punishment" that would deny extra funding to schools that needed it most.
A spokeswoman said: "This seems to completely contradict Charles Clarke's claims that he wants all schools to be specialists and will only worsen the two-tier system."