Parents of four children at £11,000-a-year Edinburgh Academy complained in April this year that their sons had returned from an adventure trip "black and blue".
It was alleged by one parent that 15-year-olds had been placed inside their sleeping bags and beaten with wire coat hangers.
Police Scotland revealed yesterday that a report concerning two 17-year-olds and a 16-year-old had been sent to the procurator-fiscal.
A police insider said that due to the severity of the incident they had charged three youths with a variety of assault and reckless conduct offences.
The source said the procurator-fiscal will now have to decide whether to take the case to an adult court. One of the alternatives could be to issue a warning and involve social workers.
The alleged incident is believed to have happened while the students were at a week-long cadet camp in the Aberdeen area in early April.
At the time parents said that they were "gobsmacked" by the incident.
A Police Scotland spokesman said: "Officers in Edinburgh have been carrying out enquiries following reports of assaults involving pupils from one of the city's schools.
"The matter, which dates back to April 2014, has been thoroughly investigated.
"As a result of these investigations and following consultation with the Juvenile Liaison Office, three boys, two aged 17 and one aged 16, will be the subject of a report to the procurator-fiscal."
The school's web page explains that the Easter camp is a "self-run Adventurous Training/Military camp usually held in Scotland and is always very popular amongst the cadets".
Speaking at the time of the alleged assault, a source close to the school said: "Just because the school has been around for more than 100 years, doesn't mean this ... is acceptable.
"When the boys and girls came back from their trip, at least four parents approached me and told me their boys were covered head to toe in bruises.
"When asked what happened, the kids told them that they had been tied up in their sleeping bags before being kicked and punched by the bigger boys.
"They didn't know if it was an initiation of sorts or if it was just the older boys, who are around 17, having 'fun' but now the parents want criminal charges brought against these bullies."
The private school - which was founded by Sir Walter Scott and counts Robert Louis Stevenson among its old boys - has an army and air cadet section.
The Easter camp is one of two events for the Army Section of the Combined Cadet Force in a year. The activities usually include "camping, self-reliance and leadership skills".
A spokeswoman for Edinburgh Academy declined to comment, saying it would be inappropriate for the school to do so at this time.