The proposal came from the committee on special needs chaired by Sheila Riddell, professor of social policy (disability studies) at Glasgow University, and was accepted by ministers last week. But they have promised to consult on the proposal, under which the cash will be transferred to local authorities.

The Riddell committee concluded that the schools drew most of their 400 pupils from the local areas, and therefore did not justify direct central government expenditure as “national centres.” After a three-year transitional period, it will be up to the authorities whether they wish to continue using the schools. If they do, they will be charged the full economic fee, from pound;9100 for a day place to pound;28,400 for residential pupils.

In its response to the Riddell recommendations, the Scottish Executive was at pains to underline the value of the schools. “Ministers are confident that if the schools continue to make high quality provision which meets the needs of children, their role will continue and expand,” the official statement said.

The Riddell report suggests the schools could support education authorities by supplying “a high level of health care or therapy, or to secure respite care.”

The report adds: “There are expectations on the part of parents that their right under legislation to exercise a choice of school for their children depends to some extent on there being some diversity of provision in the system.”

Janet Allan, the principal of Donaldson’s School for the Deaf in Edinburgh, is concerned that “if our numbers fall, we could face the prospect of laying off staff. If they then rise, we might have the problem of recruiting staff quickly in what is a highly specialist field. But we will just have to be good enough that people cannot do without us.”

Mike Martin, director of development at Capability Scotland, said they had been “reading the runes” and the decision came as little surprise.

His organisation runs two of the schools, Corseford in Kilbarchan and Stanmore House in Lanark. They have already begun to look for ways to work more closely with local authorities, such as supporting pupils in mainstream classes.

Patrick Webb, head of Harmeny School in Balerno for pupils with behavioural needs, warned that the transitional period would have to be managed very carefully to avoid any threat to the schools. “We also want to ensure the quality of provision is not watered down, so pupils will still receive the resources and facilities they need,” he said.

Lillemor Jernqvist, head of Craighalbert School for conductive education in Cumbernauld, said it was too early to say whether there was any threat to the school, although there have long been concerns that too few authorities are making use of it. But she added: “If some education authorities are not sending pupils to our schools, it is not because there is no need. It is because they don’t tell parents about the facilities we can provide.”

Kevin Tansley, head of the Royal Blind School in Edinburgh, takes pupils from almost every part of Scotland and the north of England. He believes his school will continue as a “national centre” in practice. “If the quality of education and care is of sufficiently high standard, the local authorities will continue to use us whether the funding comes from local or central government,” he said.