The move has come after a former teacher at the school, Linda McCall, was found guilty at Jedburgh Sheriff Court earlier this month of assaulting children in her care.
The initial trial of 60-year-old McCall took place last July, but Sheriff Roderick Flinn ruled at the time there was no case to answer.
However, the Crown successfully appealed that ruling, and McCall was found guilty after trial at Selkirk Sheriff Court on Thursday, May 13.
Before the meeting of the full council this morning, chief executive Netta Meadows told councillors: “As you are aware, a former employee of SBC has been found guilty of a number of criminal offences committed within a school setting.
“The welfare and safety of our young people is at the very heart of everything that we do. Therefore, as head of paid service, I feel it is important to fully understand what has occurred.
“Following discussions with the leader and the convener, I am therefore instigating an independent inquiry into how the council dealt with the concerns which were raised. This process will firstly require us to identify a suitable individual to carry out the work. I will bring a report to council in June which will provide details on the scope of the investigation, together with an expected timescale for its conclusion.
“Separately to this, I am seeking an independent review of the provision of education and of the practices followed at our complex needs settings. I have asked the service director for young people, engagement and inclusion to engage with Education Scotland to scope this review. My report in June will also provide an update on this review.
“I know that it is important to all of us that both of these matters are comprehensively considered. As I have said, the welfare and safety of our children and young people is paramount.”
The move has been welcomed by Marina Urie, a senior lawyer who represents the affected families in their civil action against the council.
She said: “The announcement of this inquiry by SBC is a very welcome development and we hope that it can get to the bottom of the mishandling of an extremely serious child protection issue.
"Children were abused by a trusted teacher who was only brought to justice by the determined actions of the families involved.
"The council have to explain why parents concerns were brushed aside in what appears to have been a concerted attempt to protect the reputation of the council and the teacher involved. We look forward to being fully included in the inquiry process.”
Christine Grahame MSP, also welcomed the setting up of the inquiry.
She said: “I welcome the confirmation of an independent inquiry from Scottish Borders Council, but I do still believe the devil is in the detail which we’ve yet to see.
“Scottish Borders Council’s earlier ‘independent’ inquiry exonerated that staff member of any fault and it took police investigations and a subsequent trial to expose the truth.
“Given that we’re talking about suspicions of a cover up within SBC, this process must be fully transparent to restore public confidence and ensure that parents of the affected children are central to the discussions on the process to have faith in its ability to get answers.
“What happened in this case is abhorrent and has left the families affected to pick up the pieces.
"Scottish Borders Council did not keep these children safe and any inquiry must get right to the heart of why this is, so it can never happen again.”