The ruling threatens to erode the rights of thousands of parents whose children have disabilities.
The Scottish Government introduced co-ordinated support plans (CSP) for pupils with additional support needs to set the levels of support they could expect from their local council.
However, the status of the plans was thrown into confusion after a court ruled last month that there was no requirement for councils to provide such support - even if it was detailed in the plan.
Following the case, a group of charities, including education provider Spark of Genius, wrote to the Scottish Government under the banner of the Scottish Children's Services Coalition.
They urged the Government it to amend the Additional Support for Learning Act and its associated code of practice.
But the response from Alasdair Allan, Minister for Learning, said it was not appropriate for ministers to comment on a decision made by a tribunal "as it would be construed as an act of interference with judicial independence."
A spokesman for the coalition group said: "It appears the Scottish Government is dodging the issue as this provides no reassurance on the status of the CSP and still leaves considerable dubiety over it.
"While it makes clear the legislation makes a significant contribution to the delivery of support, it fails to provide a clear answer over the statutory status of a CSP.
"We, as will many of those with children and young people we work with, share a concern that the CSP is hardly worth the paper it is written on and is not the guarantee of support they thought it to be."
The case centres on nine-year-old autistic pupil Thomas Lloyd, who was given a co-ordinated support plan (CSP) by Glasgow City Council, which said he would receive weekly speech and language therapy to help his communication.
Despite the contents of the CSP, Thomas was not given therapy when he attended St Kevin's special school in Springburn last year, and his family, from Broomhill in the city's west end, took the case to a tribunal.
At the hearing, the council successfully argued there was no requirement to provide the support because the pupil did not need it, despite the fact it was expressly detailed in his CSP.
In the wake of the ruling, Iain Nisbet, a solicitor with the Education Law Unit at Govan Law Centre, which handled the case, said it threatened the rights of all parents with a CSP because, if correct, it meant a CSP was effectively unenforceable.
Mr Nisbet said yesterday: "We are encouraged by the Scottish Government's position on the legally binding nature of the CSP in the letter from the minister to the coalition.
"However, while a single tribunal decision does not set any kind of precedent, we would urge ministers to take the opportunity to clarify the position and set parents' minds at ease by amending the Act or the Code of Practice."
The Scottish Children's Services Coalition comprises a number of education providers and charities including Mindroom, Spark of Genius, Who Cares? Scotland, Falkland House School and Young Foundations.