A HIQA inspection of the state's child detention facility at Oberstown in North Dublin has found that some residents were forced to spend up to nine days separated from their peers.
Two of the children were not given access to fresh air for a week during their isolation.
The centre has said improvements have been made both before and since the inspection.
The inspection of Oberstown Children Detention Campus also identified two serious risks relating to medication management and prompted the ordering of immediate action to protect a child and to ensure that medicines were stored securely.
During HIQA's pre-announced inspection last March, 35 males aged between 14 and 18 were on the Oberstown campus in rural north Co Dublin.
It is licensed to accommodate up to 54.
The facility was already being reviewed by international experts following serious riots and industrial action by staff last year.
Since the HIQA inspection, a further riot five weeks ago resulted in additional serious damage and physical threats to personnel, including campus director Pat Bergin.
Records did not describe type of restraint
Today's report of the March inspection fails Oberstown's care record, and says that not all staff adhered to its behaviour management policies.
It criticises the facility's failure to always authorise or extend "single separation" in line with policy.
HIQA says the policy should involve isolating the youths from peers in a safe and secure area to control them and minimise an extreme and immediate risk posed by the child to himself or anyone else.
The watchdog states that some children spent long periods of time in single separation and the reasons for this were not always clearly recorded.
Records did not show that restrictive practices such as single separation were used as a last resort.
The report says records of restraint did not always describe the type of restraint used.
It says that the centre's behaviour management model did not fully meet the needs of children or staff.
It adds that some individual crisis management plans were not of good quality.
Delays in hospital treatment criticised
The report also fails Oberstown's care for the health of residents.
It criticises delays in ensuring that children received hospital treatment when this was recommended by the centre's nurses.
Medicines were not always administered in accordance with prescriptions and records of the administration were not complete.
It adds that the custody of medicines was inadequate and that inspectors ordered the implementation of immediate action to protect a child from a medication-related risk and to ensure that medicines were stored securely.
Oberstown says positive developments since inspection
The director of the campus, Mr Bergin, said there is evidence of a lot of positive developments regarding the care of young people since the last inspection.
Speaking on RTÉ's News at One, he defended some of the criticisms in the report, including one that stated some children spent long periods in single separation with the reasons for this not clearly recorded.
He said: "The report said of the 148 single separation incidents the inspectors reviewed, the vast majority were appropriate considering the risks young people displayed at the time."
He added: "The key issue that the inspectors raise is how can I be assured that all of the single separations are appropriately undertaken.
"They have referenced in the inspection report that there has been significant improvements around our analysis of single separation, changes that have taken place and ensuring that single separations are compliant with the policy that was approved by the department in January."
Mr Bergin did however admit that the report identified the recording of single separation as the biggest deficit in the inspection.
He added that an Oberstown case management system is planned to be rolled out this autumn.
The acting Executive Director of the Irish Penal Reform Trust has said she is concerned about the fact some children are being held in isolation for days, rather than a matter of hours.
Speaking on RTÉ's Drivetime, Fíona Ní Chinnéide said the number of single separation incidents at the facility, that were highlighted by the report equates to 18 per child, per day, which she described as "very high".
"We'd be concerned that at most it would be a matter of hours and certainly not days that any child be held in isolation from his or her peers," she said.
"The number of incidents were over 3,000 in 2016. The inspectors focused in on 148 particular incidents, relating to eight children over a three month period. That's 18 per child, per day. That's very high."
She said there are some positive findings contained in the report, saying a strong emphasis on the participation of children, positive relationships between staff and children, and greater availability of psychological and educational supports show that there are "many good things happening at Oberstown."
However, Ms Ní Chinnéide described as "incredible" that a fire safety policy was not implemented fully "especially given that it was identified by a HIQA inspection in 2015."
She said it was a "big concern" that not all children were fully informed of fire safety, and that risks surrounding the management, and dispensing of medicine were "pretty grave stuff".