The Education Authority (EA) must be subject to an independent review after an internal audit found "unnecessary and undue" delays into its assessment process for special education needs (SEN) pupils.
Alliance MLA Chris Lyttle, who is chairperson of the Stormont Education Committee, made the call after a report was presented by the EA yesterday.
He said the report "underlines what can only be described as an appalling and distinct lack of managerial oversight and good governance".
The report found a series of failings, including the security of confidential information and unnecessary delays into the statementing process.
Sara Long, chief executive of the EA, apologised to families for the "distress and worry" caused.
Speaking before the committee, she said that the authority was guilty of "significant shortcomings".
Latest figures show that 250 children are currently waiting more than 50 weeks for assessment. Another 700 are waiting between 26 and 50 weeks to be assessed.
It has been revealed that overall there are more than 2,000 children here waiting to be assessed for medical conditions which could affect their education.
West Belfast, north Belfast and south Down are the three worst affected areas.
Sinn Fein committee member Karen Mullan described the findings as "truly shocking".
"The findings have confirmed what many of us have known for a considerable amount of time - the Education Authority has systematically failed some of the most vulnerable children in the north," she said.
"But what is truly shocking is the fact that there are some children out there waiting almost two years for a statement defining the unique support required by a child with special educational needs.
"These children have been badly let down and have had their right to education undermined by failures within the Education Authority."
Mr Lyttle said the committee will now hold the EA's improvement plan to "account".
"But it is increasingly clear a full independent review of the EA must now follow," he added.
"The welfare and development of SEN pupils should be the priority throughout this entire episode.
"The lack of communication from the EA to parents of pupils has characterised much of the statementing process."
Ms Long also stressed to the committee the delays in the SEN statutory assessment process was "unacceptable".
"They have caused distress and worry for families and they have delayed the provision of appropriate services to children and young people with Special Educational Needs," Ms Long said.
The EA chief executive said work is under way to improve the assessment process, which had already achieved a 36% reduction in number of statements taking longer than 26 weeks to complete.