The boys, aged between 14 and 18 appeared in court on Friday and were released into the care of their parents and were not allowed to speak to State witnesses.
The case was postponed to March 5.
According to the report, one of the boys could not stop crying during court proceedings.
It is alleged that a group of white boys grabbed a black boy and subjected him to inhumane torture on Sunday, education department spokesman Sydney Stander told the newspaper.
“He was stripped and painted white. After that he was sodomised with a stick. Boys who watched, cheered them on,” he said.
The department had sent a team to support the victim, his family, teachers and other pupils at the Hoër Landbouskool Noord-Kaapland.
Police spokeswoman Dimakatso Mooi was quoted as saying that the boy was stripped, his hands and feet bound, as part of an initiation process. He was then attacked.