The study, commissioned by the Scottish Executive, shows special-school populations are now skewed towards secondary-age pupils. Mainstream primaries are taking in more children with moderate learning difficulties, hearing or visual impairment, social, emotional and behavioural difficulties, and autism.
It reports a consensus that mainstream education can benefit children with physical impairments, but suggests the perceived rise in challenging behaviour in schools is related to the increase in pupils on the autistic spectrum.
The report finds that some special schools struggle to find sufficient support from therapists who now have so much work in the mainstream sector, and it suggests the Executive may need to take on a strategic planning role to ensure youngsters with special needs get more effective support.
This is supported by Ronnie O'Connor, president of the Association of Directors of Education in Scotland, who said the Executive should work on a strategic approach with the local authorities, based on "this important piece of research".
But Robert Brown, the Deputy Education Minister, said the strategic planning of schooling was a matter for local authorities. He said the Executive was willing to work with the authorities and others "to provide clarity around particular definitions".
The researchers, from the Scottish Council for Research in Education centre at Glasgow University, also found that, while there has been little change in the number of pupils attending special schools as a result of mainstreaming, there has been a major influx of secondary-age children who are now the majority in such schools. Far fewer enter at the P1 stage.
They say that this analysis "supports the hypothesis that the presumption of mainstreaming has resulted in the placement of more children with special needs in mainstream primary schools".
The Scottish Executive has consistently maintained that there has been little change in either the number of special schools or the number of pupils attending them since the presumption of mainstreaming became policy.
In response to claims from the Conservatives that mainstreaming was causing the closure of special schools, the Executive pointed out that there was only a slight decline of 0.04 per cent in the proportion of the pupil population who were in special schools from 1998-2003. There has been a further drop of 0.03 per cent since the mainstreaming duty took effect in 2003-04. However, the finding that there has been a significant change in the type of pupils attending special schools will have implications for how the mainstream sector deals with those with additional support needs.
The researchers, Anne Pirrie, George Head and Paul Brna, suggest that one possible explanation for the over-representation of older children is "that the process of ascertaining the most appropriate placement can be protracted and difficult for all parties".
One special school headteacher told the researchers: "The number of children traumatised by repeated failure in under-equipped mainstream settings is very high. Many would be able to integrate successfully if intervention was early and adequate."
The research, carried out before the Additional Support for Learning Act was implemented in November last year, also finds evidence of a perceived increase in the range and complexity of conditions catered for in special schools.
In a survey of special school heads, 32 per cent of those who said that the needs of their school populations had changed in the last five years also reported more pupils with autism, challenging behaviour, and mental health difficulties.
The headteacher of another special school told the researchers: "The range of pupils is unsuitable for one establishment. We now have potentially violent pupils alongside the most vulnerable... the range is unmanageable, and very worrying in terms of securing the safety of some of the most vulnerable."
Although the report acknowledges that there are examples of situations where the presence of a child with challenging behaviour was considered to have a deleterious effect on the rest of the class, it adds that "the broader picture is that there is no evidence from the statistical analysis of the Scottish school census data that the presence of pupils with SEN has had an effect -positive or negative - upon pupils' attainment".
George MacBride, education convener of the Educational Institute of Scotland, said the report's findings supported the union's assertion that mainstreaming can work effectively, but only if it is properly managed and adequately resourced.
He welcomed the report's finding that "there was a consensus in favour of mixed economy of provision - that is a commitment to specialist services within an inclusive model".
The research also points to the previous Conservative government as being largely responsible for encouraging mainstreaming in schools, rather than the Scottish Executive. The key catalyst was the reorganisation of local government in the mid-1990s, not the Standards in Scotland's Schools Act 2000.
This will wrong-foot the Conservatives, who have been harshly critical of the Executive's policy. Their council reforms replaced the nine mainland regional authorities with 29 smaller ones. This meant that, in four authorities (Angus, Clackmannanshire, East Lothian and Moray), specialist provision was no longer available.
In several others, including East Dunbartonshire, East Renfrewshire, Midlothian, Perth and Kinross and South Lanarkshire, there was "a substantial reduction in the number and range of specialist facilities available in the local area", the report states.
One local authority is quoted in the report as saying that, after reorganisation, "the drive to avoid placing children in residential provision resulted in mainstreaming well in advance of the legislation".
Another adds that "one of the least satisfactory aspects of the mainstreaming policy is the perception that 'inclusion' pupils are new to mainstream".
The research also finds a wide variation in practice between different authorities, including different definitions of the main "difficulties of learning".
Professor Sheila Riddell's finding in the late 1990s that "there is high mainstreaming in outlying areas, low mainstreaming in cities" remains the case. But there are also substantial variations between cities in respect of the percentage of children in specialist provision: in 2002, 33 per cent of special needs pupils in Glasgow were educated in mainstream schools, compared to 71 per cent in Aberdeen.
The Deputy Education Minister said the research "seems to indicate that in Scotland we have the balance right between mainstream and special school provision".