As the Church of England issued its Dearing Report pressing the case for 100 more Anglican secondary schools, a study highlighted the growing polarisation of poor and rich pupils as secondary schools become more diverse.
Professor Stephen Gorard, of the school of social sciences at Cardiff University, has been studying school intake data for 1988-2000. He concludes that since 1997 they have become more segregated by poverty.
"The rise of the specialist school may worsen this general situation," he warns in a draft paper presented to an Institute of Public Policy Research seminar this week.
Prime Minister Tony Blair has been impressed by data that suggests that results in specialist schools have been improving at a faster rate than in other comprehensives.
The Government trebled the number of specialist schools to more than 600 in its first term and set a target in its election manifesto of 1,500 - almost half of all secondary schools - by 2006. It says that all schools could become specialist if they meet the criteria.
But Professor Gorard's findings, based on numbers taking free school meals, suggest that the improvement could arise in part because they are taking more privileged students.
Between 199495 and 19992000, the secondary school system became more polarised, reversing the trend of previous years. Some 29 per cent of all schools became more privileged - that is, they took "less than their local fair share of children from families in poverty".
But in specialist schools the figure was 37 per cent, with the change most marked in those that controlled their own admissions - foundation schools (43 per cent) and voluntary-aided CE (57 per cent). P> Professor Gorard said: "Those schools taking an increasingly privileged intake tend to be specialist or selective or their own admission authorities. Where more than one of these is the case, the tendency is significantly enhanced."
Only local authority specialist schools - a growing proportion of the total - are broadly in line with their non-specialist counterparts.
John Bangs, head of education policy at the National Union of Teachers, said: "This evidence simply confirms what Tony Blair has been denying: that this is a two-tier system. If you grant a school specialist status, then that is a privileged status and that message goes right round the community."
But the Technology Colleges' Trust, which supports specialist schools, dismissed the findings as rubbish. Trust chief executive Sir Cyril Taylor said that free school meals were an unreliable indicator of students' backgrounds because many did not claim them, while others could be just above the qualifying line.
And he claimed that the huge increase in local authority schools joining the programme this year - many from the inner cities - meant the figures were already out of date. He predicted a "dramatic" jump in the number of pupils taking free school meals.
Canon John Hall, Church of England director of education, said he would look closely at the findings when published. "The Church set schools up in the first place to serve the poor in the community," he said. "We continue to consider that very important."
A spokeswoman for the Department for Education and Skills said there was no intention to create a two-tier system. "The assessment criteria for applicant schools gives some preference to schools in areas of deprivation, including areas covered by the Excellence in Cities Programme, which now involves more than a third of all LEAs."