Mainstream school is not for all young people and may actually damage their education and life chances, Jack McConnell said.
The Executive was in danger at one point of almost forcing children and young people into mainstream schools or creating a climate in local authorities which made it difficult to opt for special schools, the Education Minister said.
"Mainstreaming is good in theory, it is right in principle but in practice parents have to have a choice and children's reality in schools day after day taken into account," he said.
Tony Finn, head of St Andrew's High, Kirkcaldy, told him that teachers were cynical about social inclusion when they faced daily problems in the classroom.
Mr McConnell replied that a reduction in exclusions was not an end in itself. "I want to see fewer exclusions but I want to see schools run properly, our classrooms with positive learning environment and I do not want the majority of kids disadvantaged," he said.
Social inclusion was often focused on discipline and special educational needs but was still a relevant concept at a time when "thousands of working-class kids still do not achieve their full potential". Schools in disadvantaged areas and the pupils who went to them had in the past been written off but it had been shown that they could be turned around.
He again cited Braidhurst High, Motherwell - in his constituency - as a prime example.
"It was a school that was struggling five years ago and its roll was plummeting, the kids were having problems achieving and the school had problems. That school now has the second highest level of attendance in North Lanarkshire and produced a sixth-year student who got the highest grades in Scotland," Mr McConnell said.