South Australia's Health and Community Services Complaints Commissioner Grant Davies inquired into the boy's case after complaints about his treatment in 2021.
His investigation found the boy, who experienced mental health issues, was physically restrained on two occasions and held in a prone position.
Such action was against SA Health's policy guidelines and standards set by the state's chief psychiatrist.
Professor Davies also found the teen was kept isolated for more than five hours over three separate periods with each period in excess of the mandated maximum of 30 minutes.
However, the commissioner did not make a finding on a third allegation that the boy was assaulted during his time at the hospital.
Prof Davies said he did not have the legislative authority to make a ruling on such an allegation.
"There is a clear policy and standard in South Australia for use of restraint and seclusion," the commissioner said.
"This investigation found that (the patient) was subject to practices not in line with the policy and standard which is very concerning.
"It is also clear there were significant gaps in the reporting of treatment and care while in hospital, and an absence of reporting on any injuries the consumer might have sustained while being subject to restrictive practices."
Prof Davies recommended the hospital retrain all security and ward staff on the policies regarding restraint and seclusion, use charts to record any injuries sustained and retrain staff with respect to proper record keeping.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
beyondblue 1300 22 4636
12°C