"On investigation, the teachers immediately called paramedics and the police, who confirmed the bad news as they couldn't resuscitate the learner.
"Senior officials of the department visited the school and the parents of the pupil were called and were informed of the tragic incident."
Kgetjepe said his department had also dispatched a team that will offer psycho social support to pupils, the staff and the affected family.
"It is hard to comprehend something this tragic and no amount of words can describe the loss. It is hard for us and obviously harder for the family, relatives and friends. In times like these, we need each other more than any other time.
"It is therefore important that we give each other the necessary support, especially the family," said Kgetjepe.
Two in court over murder of fellow pupil
Two pupils will today appear in the Seshego magistrate's court in Limpopo for the murder of a 12-year-old boy after his body was found in a room at special school on Saturday.
Police spokesperson Moatshe Ngoepe said they were investigating a case of murder.
"Two suspects aged 16 and 14 were arrested and will appear in the Seshego magistrate's court today. It is alleged the two pupils assaulted a 12-year-old boy to death," he said.
Ngoepe said the two were also pupils at Grace and Hope Special School in Seshego Zone 1 and were allegedly found to be in the room when the incident happened.
Department of education spokesperson Sam Makondo said it was aware of the arrest of the two pupils.
Limpopo MEC for education Ishmael Kgetjepe said teachers were alerted to the incident by two pupils who shared a room with the 12-year-old that he was no longer moving and breathing.
"On investigation, the teachers immediately called paramedics and the police, who confirmed the bad news as they couldn't resuscitate the learner.
"Senior officials of the department visited the school and the parents of the pupil were called and were informed of the tragic incident."
Kgetjepe said his department had also dispatched a team that will offer psycho social support to pupils, the staff and the affected family.
"It is hard to comprehend something this tragic and no amount of words can describe the loss. It is hard for us and obviously harder for the family, relatives and friends. In times like these, we need each other more than any other time.
"It is therefore important that we give each other the necessary support, especially the family," said Kgetjepe.