Quarriers has still to make final decisions on the fate of Seafield School in Ardrossan, and two children's homes in Largs and Irvine, and their future is subject to consultation.
However the school building is already on the market through a Glasgow estate agent, and the financial viability of both Merton House, in Largs and Williamfield in Irvine is thought to depend on providing accommodation for children attending the school.
The charity is also consulting with 69 members of staff who will be affected by the closures, and while it says it will try to redeploy staff if the services close, it cannot guarantee to avoid redundancies.
Paul Moore, chief executive of Quarriers, said the proposed clos-ures were due to falling demand from local councils.
He said: "This will be an extremely anxious time for every-one associated with the school and the two children's homes.
"In the past few years, as a result of the current economic climate of austerity, demand for places at Seafield has been decreasing and is forecast to continue to do so."
There are currently 14 pupils at the school, which has the capacity to take 25.
Mr Moore added: "We have made every effort to put Seafield on a more sustainable footing. However, it has continued to lose money and is forecast to have a significant deficit over this financial year. We are simply unable to continue absorbing such losses."
Quarriers said any closures would not take place until the end of this school year and it would work with councils to ensure young people are supported. It will consult with staff and trade unions over the proposals.
Katy Clark, MP for North Ayrshire and Arran, said the announcement was devastating for all involved, bad news for the local economy and that she hoped the facilities could be kept open.
"Staff have previously agreed to cuts in wages and other terms and conditions to keep their jobs and the facility open," she added.
"The children who attend these facilities have significant additional support needs, and the potential disruption could have a major impact on their wellbeing and I cannot see how it is in their interests."
Sources within local authorities suggest Seafield School has been struggling for at least a year, but budget cuts are not to blame. One factor is an increasing reluctance by councils to send children to stay significant distances from their original homes. Many councils have also cut down on the use of residential care altogether.
However Trisha Hall, manager at the Scottish Association of Social Work, said it was important budgets did not dictate policy. She said the need of vulnerable children should take priority.
"Social work departments are under tremendous pressure to make savings," she said. "We hope the impact of the potential closu-res will be investigated in detail. It would be deplorable if closure meant no provision, leaving the children and their families without the necessary support."