Tests developed two years ago for detecting special educational needs among Welsh-speaking pupils are not being used enough, making it possible that some children are being misdiagnosed.
Meanwhile, some educational psychologists have urged primary pupils with learning difficulties from English-speaking families to switch from Welsh to English-medium schools, according to the Welsh Dyslexia Project.
This could lead to Welsh-medium schools becoming more elitist because they have fewer special needs pupils, the Assembly's education committee was told this week.
Michael Davies, of the dyslexia project, said LEA educational psychologists are not making enough use of Welsh-language screening tests developed by Bangor university's dyslexia unit, in conjunction with the project and funded by the National Assembly.
He claimed some Welsh-speaking children were being wrongly labelled as low ability because tests were instead conducted in English. "Pupils receiving their education through the medium of Welsh should be assessed through Welsh -especially those in Welsh-medium designated schools where they have had Welsh as a subject from reception class," he said.
"Assessing key stage 1 pupils in a language (English) in which they have not been taught, surely gives false results. These pupils could be diagnosed as moderate learning difficulties pupils - and not ones that are dyslexic."
The special needs teacher said that the project had also received reports of primary pupils with special educational needs moving schools as a result of potentially discriminatory advice.
Educational psychologists have advised English-speaking families who have chosen Welsh-medium schools to return their children to the English-medium sector because of their learning difficulties, he claimed.
He called on the education commitee, which is reviewing SEN policy, to look more closely at the role of LEAs and schools in pupil screening. And he said teachers should be trained to administer screening tests.
An Assembly government spokesperson said: "We see special educational needs provision in Welsh and bilingually as a matter of equal opportunity."
The Welsh Assembly's goal is for the proportion of Welsh speakers to have increased 5 per cent by 2011, and it is targeting young people in particular.
Iaith Pawb, its national action plan for Wales, published in 2002, acknowledges the right of pupils, or parents of pupils, with SEN to be taught in the language of their choice.
In a report to the education committee, the Welsh Dyslexia Project also highlights variations between the numbers of pupils diagnosed with specific learning difficulties (SpLD) compared to moderate learning difficulties (MLD). Children diagnosed with MLD are often believed to be suffering from simple low ability or learning difficulties, rather than dyslexia or dyspraxia.
Mr Davies suggested schools and LEAs may be incorrectly identifying children with specific difficulties, such as dyslexia, as having MLD.
The dyslexia project is hoping to develop an e-learning course on dyslexia in Welsh and English for parents, teachers and classroom assistants - subject to funding.