School staff and governors were accused of a number of improper actions in a document written by an anonymous source who identified themselves as a teacher at the school.
Among the complaints was the allegation that the school had colluded in the social exclusion of pupils who had created Facebook pages.
The document, seen by Third Sector, was sent to Wiltshire County Council in January, and an investigation was launched involving the council and the police.
But a statement published by the council today said: "Officers from Wiltshire Police and Wiltshire social services conducted an investigation at the school. Following this, it has been unanimously agreed by all agencies involved that no specific safeguarding issues were identified and the investigation has now concluded."
The school is run by the Wessex Schools Trust, a registered charity run by members of the Brethren, a Christian group that has a strict doctrine of separation – its members cannot eat, drink or socialise with non-members, are forbidden from watching television and listening to the radio, and can use the internet only sparingly.
A Brethren congregation, the Preston Down Trust, appealed last year against a Charity Commission decision not to grant it charitable status. The case has been heavily debated in parliament. The group has faced allegations from former members that its doctrines encourage bullying and abuse, and that former members have been prevented from having contact with their families.
The appeal was due to be heard this month, but a three-month stay has been agreed while the commission and the Brethren discuss the case.