In the run-up to the Additional Support for Learning Act coming into force next Monday, Robert Brown, Deputy Education Minister, made the pledge in a parliamentary debate on special needs.
Trading statistics rather than insults was the hallmark of last week's debate, initiated by Lord James Douglas-Hamilton, the Tories' education spokesman.
Lord James argued that there should be no "presumption" in favour of mainstreaming and that parents should have the option to choose whether their children went to special schools or not.
But he said the freedom to exercise this choice was under threat, citing statistics which showed that 33 special schools had closed since Labour came to power in 1997, a net loss of 15.
But Mr Brown accused him of ignoring stand-alone special units. His figures were that 57 schools and units had opened since 1997 while 29 had closed, a net gain of 28. He added that the proportion of children educated in special schools fell by 0.07 per cent between 1998 and 2004 - "hardly an overwhelming figure".
Mr Brown said he had difficulty in understanding Lord James's proposition "that special schools and provision in mainstream schools are in opposition. Both are needed."
He added: "It has always been made clear in legislation, guidance, debates and discussions that the mainstreaming presumption is simply a presumption - it is not an inflexible rule."
The minister said that pound;95 million was being made available this year alone for additional support needs, pound;14 million of which was directly to support the new Act. There was investment in training and support, the number of educational psychologists had reached 400 for the first time ever, there had been a 5 per cent rise in the number of speech and language therapists and a 35 per cent increase in social workers and there were targets to boost teacher numbers.
But MSPs from all persuasions needed convincing that enough was being done.
Rosemary Byrne of the Scottish Socialist Party and a former special needs teacher, said inclusion would only work with choice and smaller classes.
John Swinney, the former SNP leader, said he was "increasingly alarmed by what I hear when I talk to parents about what is in place on the ground in mainstream schools to support young people". But Mr Swinney acknowledged that mainstreaming offered all pupils the best opportunities.
Fiona Hyslop, the SNP's education spokesperson, said there was a consensus among the parties, except the Conservatives, that the presumption of mainstreaming should be supported - but resources were necessary to make a reality of the "wonderful words".
Elaine Murray, a Labour MSP and former education convener of South Ayrshire Council, pointed out that removing the presumption of mainstreaming would contravene article 2 of the UN Convention on the Rights of the Child, the right not to be discriminated against.
Mr Brown said the Tory motion "poses a dilemma that does not exist, is based on an untrue assertion about a declining number of special schools, and it raises an option that is unnecessary". It was heavily defeated.