A royal commission into child sex abuse is hearing evidence about five decades of complaints at Geelong Grammar.
Prince Charles once spent two terms at the school, although he has no involvement with this commission.
One former student said he was touched on the genitals by a chaplain and then threatened with expulsion when he reported the abuse.
"You're really lucky... we didn't believe you, but [the chaplain] confessed," he said staff told him.
Referred to as BKO by the commission, the witness described the school's Timbertop camp, where Prince Charles spent two terms in 1966, as similar to Lord of the Flies.
In William Golding's novel, a group of schoolboys stranded on an island turn against each other, with deadly consequences.
BKO said the school in Victoria was concerned only with avoiding scandal, rather than stopping the abuse.
Local media report that another former student, described as BKM, told the commission that Geelong Grammar should repay the fees of abuse victims.
"They made my father pay an exceptional amount of money," he said.
"I was sexually abused, and repeatedly and seemingly uncaringly, re-exposed to the situation that allowed the abuse."
In a statement issued last week, the current principal of Geeolong Grammar, Stephen Meek, said the school "absolutely condemns any form of abuse... that has occurred at the school in the past."
"I greatly regret that not all of our students received the care and support to which they were entitled," he added.
Former pupils of elite Australian school have told an inquiry that their abuse claims were ignored for decades.