Two children in a special care unit had to urinate on the floor because they were not allowed to use the toilet, inspectors found.
The children, who were being cared for in a "safe" room at Ballydowd Special Care Unit in Lucan, Co Dublin, were prevented from using the toilet on the basis of risk to themselves, the Health Information and Quality Authority (HIQA) has disclosed.
However, inspectors who visited the facility for troubled children aged 11 to 17 in July said "the actual risk was not clearly defined".
They said: "In interviews with inspectors, one child described not being allowed access to a toilet as 'disgusting'. Another young person did not have access to a shower until day four of a five-day period of continuous single separation.
"Instead, the young person was provided with baby wipes. On exploration of this practice, inspectors found that a secure door was placed into the toilet alcove to prevent access as it was a 'blind spot' and therefore a child could not be seen by staff members during observations from the corridor.
"For some children, the risk was that they could engage in self-harm. The flaws in the design of a room should not justify these practices and children should have appropriate access to a toilet and shower facility during single separation."
Records show three children in single separation had slept without a mattress or blankets on numerous occasions in the past two months because they tore them up and tried to self-harm.
"From interviews and a review of records, inspectors found that this occurred due to concerns about children harming themselves by creating ligatures from torn mattresses and blankets," the report said.
The service was struggling to provide adequate care for one young person in particular because of concerns about their behaviour.
Some of the children were separated from others and placed in the safe room for 24 hours and, in one case, it lasted for five days.
Children also did not have access to fresh air or exercise while they were separated.
Fred McBride, the chief operations officer at Tusla, the Child and Family Agency, said it accepted that on occasion, faced with intense and sustained pressure from challenging and violent behaviour, the processes underpinning the use of single separation were not adequate.
Toilet access was restricted when a risk assessment determined they were unsafe due to indications of self-harm.
It was in the process of developing a specially designed single-occupancy facility at Ballydowd that would be better equipped to deal with extremely challenging behaviour and which would reduce the need for single separation.
The agency is commissioning research on how to better understand a sudden eruption in challenging behaviour.