Children as young as five with disabilities are being secluded and restrained at school.
A new report from Inclusion Ireland highlights 14 cases, one involves a child being left unsupervised in seclusion for long periods despite a history of seizures.
The charity says that a lack of available research on the subject means the number of cases of restraint, isolation and seclusion could be even higher.
They are calling on the Government to act and spokesperson, Mark O'Connor, has said there are a number of key areas which need to be looked at.
Mr O'Connor said: "Regulation, inspection and monitoring of this issue. Currently, as we stand, there is no need for a school to report anything.
"Training for staff so that these incidents are reduced to the absolute minimum and then the appropriate services for children.
"Child and adolescent mental health services, speech and language therapy, psychology, all of those types of services should be immediately available to a child who is experiencing these situations."
He described some of the incidents brought to their attention.
He said: "What families are telling us is that some children as young as five have been locked into rooms in schools and have been physically held down.
"Not always for behaviour issues, there are different instances where one child was restrained in a wheelchair every time there was a school outing. This was a child who was fully able to walk."
One parent described how her child had their head held down between their knees for 20 minutes during a bus journey, another child was locked in an unattended room for up to five hours and another was left unsupervised in seclusion for long periods - despite a history of seizures.
Paddy Connolly, CEO of Inclusion Ireland, said: "The rights and welfare of children should be at the centre of all that happens in schools.
"On the issue of managing the use of seclusion and restraint, best practice includes support and training for staff, whole of school positive behaviour strategies, school leadership and external inputs such as child mental health or disability services.
"It is unfair on teachers and a neglect of children's developmental and welfare needs that the department continues to ignore this issue.
"It leaves teachers exposed, isolates parents and adversely impacts on the mental health and education of the children concerned."
"Ireland's record in relation to children with disabilities in general is shameful, whether it's the disarray of the assessment of need system, their exclusion from personalised budgets or failures in the education system, it's true to say that this Government is failing children with a disability."
Inclusion Ireland has made a number of recommendations - including that the Department of Education take steps to ensure that seclusion and restraint become a matter of last resort, measures are taken to include guidelines and monitoring to tightly prescribe the use of seclusion and restraint, and there is raining to monitor, support and supervise staff using restrictive practices.