Queen Victoria School (QVS) is one of 17 additional institutions to be included in the national inquiry led by judge Lady Smith.
The Dunblane school, which serves the families of military personnel, has previously been linked to Thomas Hamilton, who killed 16 pupils and their teacher at Dunblane Primary School in 1996.
Last year, Glen Harrison, a former housemaster, claimed pupils were abused by a paedophile ring at the school in the 1980s and 1990s. He said he first raised his concerns with police in 1991.
The national inquiry, which has cost £15.7m to date and is looking at the historical abuse of children in care, announced on Thursday a list of extra investigations, taking the total number of institutions being looked at to 86.
The institutions announced yesterday include the Royal Blind School and Donaldson’s School for the Deaf in Edinburgh.
Lady Smith appealed for anyone with information about any of the institutions on the list to get in touch with the inquiry.
She said: “It does not matter whether you have already made a report to the police or to anyone else and it does not matter whether or not you have been involved in any other investigation. You can still talk to us and we want to hear from you.
“I am well aware that it can be difficult and very emotional to talk about experiences in care and I want to take this opportunity to give an assurance that we have a dedicated witness support team here who will help and support anyone providing evidence to us. They will do so throughout the process.”
It has previously been claimed that Hamilton was linked to the a paedophile ring and was a frequent visitor to QVS.
The school did not respond to a request for comment yesterday, but a spokeswoman for the Ministry of Defence (MOD), which funds the school, said: “All historic allegations of sexual abuse involving Queen Victoria School were reported to the police at the time.
“We take any allegations of this nature extremely seriously and always co-operate fully with any police inquiry.”
The national inquiry, which began its work in 2015, has so far looked at allegations of physical and sexual abuse at institutions run by female religious orders.
It is due to deliver a report in the coming weeks on abuse at Smyllum orphanage in Lanark where children were allegedly beaten, force-fed and humiliated for wetting the bed prior to its closure in 1981.
Last month Police Scotland said eleven women and one man, aged between 62 and 85, had been charged in relation to non-recent abuse at the orphanage.
Earlier this year, it was announced that the time-frame of the inquiry would be extended indefinitely to allow more survivors to come forward and give evidence.
A TV advertising campaign, which hopes to encourage survivors in greater numbers, will be aired later this year.
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The inquiry’s public hearings, which begin again next month, will now look at institutions run by Quarriers Homes, the Aberlour Child Care Trust and Barnardo’s before turning its attention to homes run by male religious orders.
There will also be a case study looking at child migrant schemes, where children were sent to countries including Australia and Canada.
Among the other institutions announced yesterday is Lennox Castle hospital near Glasgow which closed in 2002 and where it’s alleged children were experimented on as part of a drugs programme run by Porton Down research laboratory during the Cold War.
Campaign group In-Care Abuse Survivors (Incas) has previously called on the inquiry to “review medical experimentation that was carried out on vulnerable children and adults without consent”.
Lennox Castle was one of four Scottish institutions alleged to have been involved in trialling drugs on children.
The MOD has said it is “not aware” of such tests and has seen no evidence to back up the claims. Survivors have also claimed that six and seven-year-olds were tied to racks and given electric shocks.
Anyone wishing to contact the inquiry can do so by calling 0800 0929 300 or by email to: [email protected]