The HSE has failed to assess almost 3,500 children for special needs within the six-month timeframe set down by law.
An 'assessment of need' allows children to be diagnosed with a disability, such as autism, so they can access the care they need.
Under the Disability Act, the HSE is supposed to complete the assessments within six months.
According to new figures released to Newstalk however, that target is not being met in many cases.
At the end of September, almost 3,500 special needs assessments for children with disabilities were legally overdue
Some 2,193 of the child special needs assessments were at least three months overdue – including 478 in Cork and Kerry.
Donegal GP Ciaran O'Fearraigh said the delays are unacceptable.
“It is a big problem because a lot of these are young children and we are trying to get to a diagnosis and without a diagnosis they can’t access the care that they need,” he said.
“We know that, from the evidence, early assessment and early intervention can improve outcomes so any delay in that assessment can lead to poorer outcomes for children unfortunately.”
He said the children are assessed for many reasons – and delays are very concerning for parents.
“Sometimes it is things like delays with their speech or their behaviour isn’t as expected,” he said.
“So obviously it is concerning for parents if a healthcare professional raises a concern and they want to get their child assessed as quickly as possible.”
462 assessments in north Dublin are at least three months late, according to the HSE latest figures.