The Otago Daily Times understands three boys have been stood down from St Kevin’s College hostel following the incident.
A fourth boy, the alleged victim, has remained in the hostel with parental support.
A source described the incident as "waterboarding".
"A boy at the junior hostel was waterboarded and stripped down to his undies," they said.
The school said in a statement it was taking the situation seriously.
"St Kevin's hostel has acted swiftly and decisively following a serious bullying incident at the hostel.
"The incident was reported immediately, and those allegedly involved were stood down from the hostel as part of our rigorous response protocol.
"Hostel leadership provided immediate and ongoing support to the victim’s family, assisting them in reporting the matter to the police and is continuing to support the young person within the hostel environment.
As the incident was now under active police investigation, the school could not provide further comment.
"Our priority remains the safety and wellbeing of our students and fully co-operating with the authorities."
The school was unable to provide any further details or facts that could identify either the alleged victim or those who did the bullying.
Police have been approached for comment.
Ministry of Education data shows 476 students attended the Catholic co-educational secondary school for years 9 to 13 last year.
The school’s website said the school’s hostel students arrived on Sunday, January 25, for the start of the school year the following day.
Three years ago, the Teachers Disciplinary Tribunal found the then-assistant principal and director of boarding at the school, Justin Fowler, guilty of serious misconduct when he asked two students to apprehend egg-throwing intruders on school grounds in 2020.
That incident, which resulted in a St Kevin’s student tackling an 18-year-old and breaking their collarbone, was part of a long-running rivalry between St Kevin’s and nearby Waitaki Boys' High School in relation to the Blood Match — an annual first XV rugby fixture.
