Christine Gilbert was due to tell almost 2,000 teachers from specialist schools across England that there was little evidence their status was any guarantee of improved results.
The Ofsted head also criticised schools for not using their supposed expertise in one subject to improve standards elsewhere.
She was due to make the surprise attack in Birmingham at the annual conference of the Specialist Schools and Academies Trust, which has seen a rapid rise in membership.
The schools have formed a major part of government education policy for more than 10 years. At least 90 per cent of secondaries, around 2,800 schools, are now specialists.
Ms Gilbert praised some as "exhilarating examples" of innovation and effective teaching. These included St Mary's Catholic High School in Chesterfield, which has linked up with a charity in a French-speaking community in Burkina Faso, and Chenderit School in Northamptonshire, a visual arts college that has opened a community gallery.
Ms Gilbert said she had concerns about the overall impact. "Across a range of subjects inspectors reported that they visited some schools where there was little to suggest that specialism had made a difference in terms of the fundamentals of classroom teaching.
"This is a serious criticism. If teaching had not improved, it's hard to see that learning would."
Ms Gilbert also criticised subject leaders. "We were not always impressed by the work of the subject leader in the specialist subject, particularly - and this surprises me - in terms of the quality of the subject itself, or its influence in the wider curriculum and beyond."
Specialist schools receive extra funding to improve standards. Each school is responsible for raising pound;50,000 in sponsorship, then they receive about pound;600,000 in government funding over four years.
Ms Gilbert said the benefits of the money needed to be discounted when looking at effectiveness.
Some schools had set targets which were not challenging enough, she said, while others had pursued short-term gains at the expense of long-term development.
She praised partnership work between secondary and primary schools, but said there were examples where it had distracted them from the main issues they faced.
Academics from Staffordshire and Cambridge universities said earlier this year that, after variables were taken into account, specialist schools did not get better GCSE results than comprehensives.
Speaking to the conference on Wednesday, Sir Cyril Taylor, SSAT chairman, praised specialist schools for their exam performance. Provisional results for 2007 showed 62.3 per cent of pupils achieved five good GCSEs compared with a national average of 61.5.
Speaking to the conference via a pre-recorded message, Gordon Brown, the Prime Minister, repeated his call for every school to exceed the 30 per cent barrier within five years.
Sir Cyril said a renewed focus on literacy was needed in secondary schools, and that all secondaries should give new pupils reading tests and employ specialist teachers to help struggling pupils.
School libraries should be expanded, with secondaries stocking at least 10 books per child, and local authorities should consider moving public libraries into schools to encourage children to read, he said.