Ofsted's chief inspector for England has said the government's flagship specialist school scheme has not improved teaching standards.
More than 80% of England's secondary schools now specialise
Christine Gilbert said extra resources given to such schools were "no guarantee" of higher standards.
She told the Specialist Schools and Academies Trust (SSAT) there should be a debate about the scheme's impact.
The government says specialist schools have out-performed other comprehensives on a range of measures.
Ms Gilbert's warnings came as Schools Secretary Ed Balls announced an extra £50m would be spent on the specialist schools programme over the next three years.
During a speech in Birmingham to the SSAT's annual conference, Ms Gilbert said: "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.
"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."
One inspector had warned that in "most" specialist science schools "it was not clear how the science specialism was being used to promote higher standards in the rest of the school", she said.
In some schools "the pursuit of short-term gains has been at the expense of sustained development", she added.
However, she did acknowledge that specialist schools had achieved some degree of success in fulfilling their aims of establishing a distinctive identity, working to their strengths, delivering effective teaching and learning and driving innovation.
She said inspectors had found examples where distinctiveness, innovation and improvement are being achieved.
She went on to emphasise the importance of the role of head teachers and school leaders.
She said: "Specialism has given schools extra resources which can enhance distinctiveness and improve opportunities for pupils.
"But it is only in schools where leadership and management are strong, where teaching and learning are good, that specialist status transforms provision."
There are now 2,779 specialist schools - 86% of all secondaries in England.
They receive extra government funding and private sponsorship to specialise in a particular subject area, such as music, sport, technology, languages or science.
Some specialist schools can select up to 10% of their pupils by "aptitude" for their subject.
Ms Gilbert's comments followed research criticising the specialist schools policy.
A Lancaster University report earlier this month accused ministers of a "substantial misallocation of public funds" after finding that specialist schools had made "very little impact" on results.
In September, early findings from a study by Staffordshire and Cambridge universities found that being a specialist school made no difference to GCSE grades.
In a speech to the conference following Ms Gilbert's remarks Mr Balls said: "Across the country over the past 10 years specialist schools have produced excellent results.
"Your actions demonstrate both our commitment to excellence for all and our determination to break the link between poverty and attainment which has scarred our country for so long.
"That is why we want every secondary school to be a specialist school, a trust or an academy - and every one of them will have a university or a business partner."
Shadow schools minister Nick Gibb said the specialist schools programme had not delivered "the higher standards our education system so desperately needs".
He added: "We need to ensure that the best practice adopted by the top 100 state schools is spread to all comprehensive schools in the country.
"That means high-quality teaching, setting children by ability, a strict school uniform policy, zero tolerance of bad behaviour, and a full range of extra-curricular activities."
A Department for Children, Schools and Families spokesman said that specialist schools had "delivered significant improvements in standards" and "out-perform other comprehensives".
He said: "Last year's GCSE results show that 60.6% of pupils in specialist schools achieve five A*-Cs compared with 48.3% of pupils in non-specialist schools."