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And now a motion of no confidence in council chief executive Andrew Kerr has been tabled for Thursday’s full council meeting.
The detailed findings have not been made public, but it is understood the report highlights inappropriate restraint, assaults on young people, abusive language, children being isolated and a toxic management culture.
It is also said to refer to children with bruised faces and children with burn marks where they had been restrained.
The incidents dated back more than a decade and continued right up to the end of 2019.
And the report concludes there were "failings at all levels of management".
The investigation was launched after an anonymous complaint was made in 2020 to the chief social work officer and the council's Safecall whistleblowing line, alleging serious malpractice in Edinburgh Secure Services (ESS), the section of the Children and Families department responsible for the city’s secure units, Howdenhall and St Katharine’s.
The full report has only been made available for councillors to read on a confidential basis and it is due to be discussed on a private agenda at the full council meeting.
But a summary report by council monitoring officer Nick Smith, which is on the public agenda, says the investigation identified "serious failings which compromised the wellbeing and safety of young people" over a period of more than 10 years.
It says ESS has produced a "robust and detailed action plan" to address the shortcomings.
And it contains several pages of detailed recommendations on issues such as restraint and physical intervention, allegations and complaints, recruitment, use of locum staff, quality assurance, culture and practice and management oversight.
The report comes after top QC Susanne Tanner’s investigation last year into the Sean Bell case, where an old boys’ network in the Children and Families department allegedly covered up for the former senior social worker who was a serial sex abuser, and Ms Tanner’s wider review which found “there is not a universally positive, open, safe and supportive whistleblowing and organisational culture for the raising of and responding to concerns of wrongdoing within the council”.
Conservative group leader Iain Whyte said there was “ample evidence” the failings in the secure units identified in the latest report had been known about before but the action needed to resolve them was not driven through.
"There was a previous external review and an action plan resulting from that but its recommendations were poorly implemented or ignored.
"These children are the most vulnerable in society and they are put in our care. They should be looked after. And regardless of what has got them to that stage they need the utmost respect, so these services have to make sure they are fully above board in everything they do and it is shocking to find that has not been the case in a facility run by this council.”
He said it was against the background of the Tanner reports together with other concerns and the latest report on the secure units that the Tory group had decided to table their motion of no confidence in Andrew Kerr.
Councillor Whyte said: “Publicly and privately he has been telling us for some years that he has fundamentally changed the culture in getting to the bottom of all these things.
“My concern is the culture of the council hasn't changed over the last six years with Andrew Kerr in charge. He keeps assuring us everything has changed already, it's all historic and there's nothing going on now and we keep hearing of more things coming out as whistleblowers are finally being listened to.
“We fundamentally don't have confidence in him to lead the cultural change that is needed if we're going to make the public believe that the council is doing a good job on this and properly protecting people.”
A council spokesperson said: “Following a referral to our independent whistleblowing service, an investigation identified significant failings into practices and activities within Edinburgh Secure Services.
“We want to apologise to the young people affected by this and praise those who contributed to the investigation.
“Their testimonies helped to inform the findings and recommendations, which are now being taken forward as part of a robust and detailed action plan. Significant changes are already in place and we are confident children and young people are now safer and better supported.
“Susanne Tanner QC and her review team were satisfied that this matter, once raised, was progressed appropriately through the relevant processes and both Safecall and Police Scotland were involved, providing independent oversight and demonstrating the importance and effectiveness of the whistleblowing process.”