MSPs briefly rehearsed the arguments over their future but did not issue a recommendation. It effectively ignored the issue, according to Brian Monteith, the Tories' education spokesman and a member of the committee.
Mr Monteith said the future for the schools looked "grim" since money going to authorities will not be ring-fenced and could be spent on roads or other services.
He added: "Without the grant aid, some of the schools will either face closure or some will have to put their fees up enormously or some might have to go completely private, which is all very ironic in the light of all this guff we hear from new Labour about social inclusion."
Mr Monteith will press ministers to rescind their decision or guarantee the schools' financial stability when the committee's report is debated before the full Parliament. A similar motion he tabled last year attrated support from MSPs in other parties.
Capability Scotland, which runs three special schools of which two are grant-aided, accused the committee of fudging the issue. It pointed out that Stanmore House in Lanark, one of its schools, has children from 16 different local authorities.
Sandra Kerley, the organisation's director of children and young people's services, commented: "It isn't hard to imagine the impact on strategic planning and provision if we have to negotiate with all of those authorities separately, or if they start to withdraw pupils."
Patrick Webb, head of Harmeny School in Balerno which takes in pupils with emotional and behavioural problems, also took issue with the committee's "side-stepping" stance. "Why change a situation that works until you know the alternatives are going to work? Why create a vacuum?" Mr Webb and Capability Scotland support inclusion. But Mr Webb said: "There is always going to be a need for highly specialist provision. And the fact is that there are a great many teachers out there who are simply not coping with included pupils, especially those who have serious behavioural difficulties."