This, it says in a report published on Monday, is leading to inconsistencies in the implementation of the act's code of practice.
In response, Adam Ingram, the Children's Minister, said he planned to review the legislation early next year in the light of inconsistencies across local authorities. The disparity between the number of co-ordinated support plans that had been set up was "unacceptable".
The chances of being given a CSP ranged from 1 per cent to 34 per cent across authorities - a situation which was "just not good enough", he said. "It's clear that some councils still need to do better when it comes to meeting their duties under this act, and I will write to chief executives to remind them of their responsibilities."
A third of local authority officers, as well as most parents and staff from voluntary agencies, expressed concern at the low number of co-ordinated support plans which had emerged in the transition from the former system of records of needs.
Almost all authorities had experienced difficulty defining the term "significant" and its links to determining eligibility for a co-ordinated support plan. Most authorities were unclear about whether the terms "complex" and "multiple" meant the same as "significant", it added.
In the two years since the act came into force, authorities had taken significant steps towards ensuring that children receive a personalised education. Dispute resolution arrangements were well-established in most authorities. Inspectors also came across improved partnership working between agencies and schools, which was particularly effective at the pre-five stage.
But the picture was different for young people beyond school age who required support. "In particular, through care and after care arrangements for children and young people with learning disabilities and looked after and accommodated children were unclear.
Graham Donaldson, senior chief inspector of education, called on the Scottish Government to provide additional guidance to authorities on interpretation of the legislation. "One aim of any further or improved guidance must be to achieve a fairer and more consistent approach to managing decisions about co-ordinated support plans for all who need them," he said.
Tam Baillie, assistant director of policy and influencing at Bardnardo's Scotland, said: "The findings of the report reflect our own experiences of patchy implementation across Scotland."
Barnardo's recognised the efforts being made in some areas, but remained concerned about pupils with emotional, social and behavioural difficulties and those who are being looked-after, he said.
The inspectorate has also published a new report, Count us in: achieving success for deaf pupils, intended as guidance for teachers of deaf pupils. It calls for improvements in the level of skill among communicators and teachers in British Sign Language to give deaf pupils better curriculum access.