The warning comes after new figures show significant discrepancies in the proportion of pupils identified with additional support needs (ASN) in different council areas.
Figures from the 2013 national pupil census show only 5% of pupils in primary schools in North Lanarkshire were identified with ASN, compared with 29% in Glasgow.
East Dunbartonshire records that 18% of pupils in primary and 17% in secondary have ASN, while its neighbour West Dunbartonshire records 33% in primary and 39% in secondary.
The Scottish Children's Services Coalition (SCSC), a group of educators dealing with young people with learning difficulties, has now written to the Scottish Government calling for action.
They believe the discrepancies are due to local authority inconsistencies in identifying and recording those with ASN, and fear many pupils are missing out on crucial help.
The organisation wants to see councils record more reliable information and stricter guidance from the Scottish Government.
Sophie Pilgrim, director of Kindred, a member of the SCSC, said: "We find it increasingly frustrating that we simply cannot get precise figures on the number of children with ASN and this raises concerns as to whether some local authorities are fulfilling their statutory requirements.
"This inconsistency in gathering information on and identifying those with ASN by local authorities requires clearer and comprehensive guidance from the Scottish Government.
"The Scottish Government must commit to working more closely with councils to tackle this and develop a universal method to ensure that better information is recorded so that accurate numbers can be reported. Only then will we truly be able to provide the best support for some of Scotland's most vulnerable people."
Liz Smith, Scottish Conservative spokeswoman for young people, said not enough was known about the different categories of additional needs and how numbers were changing.
She said: "The suggestion that local authorities are taking different approaches to identifying pupils with additional needs is extremely troubling. To get a true picture, there needs to be closer working across the board, with clear guidelines and a robust recording mechanism in place."
Kezia Dugdale, education spokeswoman for the Scottish Labour Party, added: "It would appear there are clear discrepancies in children being identified with ASN in different parts of Scotland.
"We need to understand why this is and we need to ensure that teachers, schools and parents are able to both identify children with additional needs and to ensure that they ask and receive additional support."
However, Douglas Chapman, education spokesman for council umbrella body Cosla, said there was no evidence pupils were not getting the required support.
He said: "As with many other statistics, we know that what has been collected over the years has changed, and this is reflected in the numbers quoted. Rather than cherry picking certain statistics, they should be more concerned about the day to day support provided in the classroom and elsewhere by dedicated professionals."
A Scottish Government spokesman said: "The recording of data about additional support for learning is the best that it has ever been due to improved recording and quality assurance.
"We have said that we would consider any evidence the coalition can provide to assist this and look forward to receiving that."
Under the Education (Additional Support for Learning) (Scotland) Act 2004 a statutory duty is placed on councils to identify, provide for and review the additional support needs of their pupils.