The warning comes after a major report on the way pupils with dyslexia are educated found many councils do not keep detailed records.
The report by curriculum body Education Scotland said: "Whilst a minority of local authorities were able to provide numbers of children with dyslexia, most did not.
"Reasons given included the numbers are not known, the authority does not record the number of pupils with dyslexia, and the authority asks schools to identify needs, but not to categorise them."
The report went on to call for councils to provide "consistently reliable" data on the number of children identified as having dyslexia in future.
Cathy Magee, chief executive of Dyslexia Scotland, said councils needed to improve the way they supported dyslexic pupils.
She said: "All children and young people with dyslexia must be given the opportunity to reach their full potential wherever they go to school and we have concerns about the inconsistency and variability of practice identified in this report.
"The way councils collect data is very varied and we are concerned because often we don't have evidence to show how pupils are being identified and supported.
"Clear guidance is needed on what data should be collected and how it should be used to ensure the same standards apply across Scotland.
"It can be very frustrating for parents who often don't know what support is available or even whether their child's needs have been assessed."
Dyslexia, which leads to pupils having difficulties with reading, writing or spelling, can be a significant barrier to learning without appropriate support.
Dyslexia Scotland has already produced an online resource for teachers, the Addressing Dyslexia Toolkit, which provides information on assessing literacy difficulties and strategies to help pupils.
Michael Russell, the Education Secretary, said progress had been made, but there was more to be done to improve support for those with dyslexia.
He said: "This report is our starting point to make sure that, regardless of where in Scotland you are or what school you go to, dyslexia does not prevent you from seizing opportunities and realising your full potential."
Dr Bill Maxwell, chief executive of Education Scotland, said the findings showed schools were getting better at working with children with dyslexia.
He said: "Teachers are better equipped than ever before and this is having a positive impact on these learners, but we will not be complacent and more work is to be done."
The Education Scotland report also called for better training of teachers. It said: "Staff in primary schools need to develop a consistent understanding of dyslexia, which may be supported by adoption of the definition of dyslexia.
"Teachers would benefit from increased professional learning opportunities relating to making appropriate provision for children with dyslexia.
"Children would benefit from a greater consistency of approach in the identification of dyslexia."
However, the report noted all local authorities now have intervention and assessment processes in place which let teachers assess learners' needs, including dyslexia.
"Beyond this,there are several differences in how local authorities identify children and young people with dyslexia.
"Most local authorities have some form of dyslexia policy or practice guidelines for schools to encourage a consistency of approach in dealing with this need.
"Not all local authorities have adopted the definition used by the Scottish Government and a few authority working groups are still debating what their definition of dyslexia should be."