Of the 424 schools surveyed, 25% said they were waiting more than nine months to have pupils assessed and some were waiting years.
"Students that require psychological assessment should be seen within one month of the assessment being requested, with six weeks being the maximum permitted waiting time," said Fine Gael's spokesperson on Education and Science, Olwyn Enright.
And with the National Educational Psychological Service only getting a 1% increase in funding in the last budget a net decrease in reality the unacceptable assessment delays looked set to continue under the Government, said Ms Enright.
General secretary of the Irish National Teachers' Organisation (INTO), John Carr, said more than 6,000 primary school children, already assessed as needing extra teaching support, were still waiting because the necessary resources had not been provided.
"Many of these applications are outstanding for nearly a year. If these children were patients on a waiting list for health services there would be a national outcry. If these children were on trolleys in a hospital corridor waiting for a bed or to see a consultant there would be uproar," said Mr Carr.
The Minister for Education and Science, Noel Dempsey, refused to comment on the Fine Gael survey.
Mr Carr said the system was overly centralised and unnecessarily bureaucratic. It was also clearly unable to respond effectively and quickly to identified needs in schools.
The INTO believes that the only way primary schools can respond to children's needs is to provide all schools with a special staffing allocation.
Acting general secretary of the Association of Secondary Teachers Ireland (ASTI), John White, said it was now Government policy to mainstream pupils with special needs but they were not supplying schools with the staffing resources to cope with this change.
"Schools are operating under increasingly crushing burdens," said Mr White, who welcomed the decision by Fine Gael to highlight the issue.
Ms Enright said the National Educational Psychological Service was dealing with 5,000 applications made by schools up to August last year. Since the beginning of the school year, a further 2,400 applications had been submitted.
"The department hasn't even worked out yet how they are going to deal with the 2,400 applications from an administrative point of view. They are all sitting untouched in a bundle," she said.
Ms Enright said the department's special education section only answered phone calls made by parents three days a week.